IL-1 zeta, IL-1 zeta splice variants and Xrec2 DNAs and polypeptides

ABSTRACT

The invention is directed to novel, purified and isolated IL-1 zeta and Xrec2 polypeptides and fragments thereof, the nucleic acids encoding such polypeptides, processes for production of recombinant forms of such polypeptides, antibodies generated against these polypeptides, fragmented peptides derived from these polypeptides, and uses thereof.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.09/876,790, filed Jun. 6, 2001, now allowed, which is acontinuation-in-part of International Application PCT/US99/29549, withan international filing date of Dec. 14, 1999 and published in Englishon Jun. 22, 2000; and claims the benefit of U.S. provisional Application60/164,675, filed on Nov. 10, 1999, and U.S. Provisional Application60/112, 163, filed Dec. 14, 1998.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The invention is directed to novel, purified and isolated IL-1 zeta,IL-1 zeta splice variants and Xrec2 polypeptides and fragments thereof,the nucleic acids encoding such polypeptides, processes for productionof recombinant forms of such polypeptides, antibodies generated againstthese polypeptides, fragmented peptides derived from these polypeptides,and uses thereof.

2. Description of Related Art

Interleukin-1 (IL-1) is a member of a large group of cytokines whoseprimary function is to mediate immune and inflammatory responses. Thereare five known IL-1 family members which include IL-1 alpha (IL-1α),IL-1 beta (IL-1β), IL-1 receptor antagonist (IL-1ra), IL-1 delta (IL-1δ)as disclosed in US/99/00514), and IL-18 (previously known as IGIF andsometimes 1L-1 gamma). IL-1 that is secreted by macrophages is actuallya mixture of mostly IL-1β and some IL-1α (Abbas et al., 1994). IL-1α andIL-1β, which are first produced as 33 kD precursors that lack a signalsequence, are further processed by proteolytic cleavage to producesecreted active forms, each about 17 kD. Additionally, the 33 kDprecursor of IL-1α is also active. Both forms of IL-1 are the productsof two different genes located on chromosome 2. Although the two formsare less than 30 percent homologous to each other, they both bind to thesame receptors and have similar activities.

IL-1ra, a biologically inactive form of IL-1, is structurally homologousto IL-1 and binds to the same receptors. Additionally, IL-1ra isproduced with a signal sequence which allows for efficient secretioninto the extracellular region where it competitively competes with IL-1(Abbas et al., 1994).

The IL-1 family of ligands binds to a family of two IL-1 receptors,which are members of the Ig superfamily. IL-1 receptors include the 80kDa type I receptor (IL-1R1) and a 68 kDa type II receptor (IL-1 R1).IL-1 ligands can also bind to a soluble proteolytic fragment of IL-1RII(sIL-1RII) (Colotta et al., 1993).

The major source of IL-1 is the activated macrophage or mononuclearphagocyte. Other cells that produce IL-1 include epithelial andendothelial cells (Abbas et al., 1994). IL-1 secretion from macrophagesoccurs after the macrophage encounters and ingests gram-negativebacteria. Such bacteria contain lipopolysaccharide (LPS) molecules, alsoknown as endotoxin, in the bacterial cell wall. LPS molecules are theactive components that stimulate macrophages to produce tumor necrosisfactor (TNF) and IL-1. In this case, IL-1 is produced in response to LPSand TNF production. At low concentrations, LPS stimulates macrophagesand activates B-cells and other host responses needed to eliminate thebacterial infection; however, at high concentrations, LPS can causesevere tissue damage, shock, and even death.

The biological functions of IL-1 include activating vascular endothelialcells and lymphocytes, local tissue destruction, and fever (Janeway etal., 1996). At low levels, IL-1 stimulates macrophages and vascularendothelial cells to produce IL-6, upregulates molecules on the surfaceof vascular endothelial cells to increase leukocyte adhesion, andindirectly activates inflammatory leukocytes by stimulating mononuclearphagocytes and other cells to produce certain chemokines that activateinflammatory leukocytes. Additionally, IL-1 is involved in otherinflammatory responses such as induction of prostaglandins, nitric oxidesynthetase, and metalloproteinases. These IL-1 functions are crucialduring low level microbial infections. However, if the microbialinfection escalates, IL-1 acts systemically by inducing fever,stimulating mononuclear phagocytes to produce IL-1 and IL-6, increasingthe production of serum proteins from hepatocytes, and activating thecoagulation system. Additionally, IL-1 does not cause hemorrhagicnecrosis of tumors, suppress bone marrow stem cell division, and IL-1 islethal to humans at high concentrations.

Given the important function of IL-1, there is a need to identifyadditional members of the IL-1 ligand family and the IL-1 receptorfamily. In addition, in view of the continuing interest in proteinresearch and the immune system, the discovery, identification, and rolesof new proteins and their inhibitors, are at the forefront of modernmolecular biology and biochemistry. Despite the growing body ofknowledge, there is still a need in the art to discover the identity andfunction of proteins involved in cellular and immune responses.

In another aspect, the identification of the primary structure, orsequence, of an unknown protein is the culmination of an arduous processof experimentation. In order to identify an unknown protein, theinvestigator can rely upon a comparison of the unknown protein to knownpeptides using a variety of techniques known to those skilled in theart. For instance, proteins are routinely analyzed using techniques suchas electrophoresis, sedimentation, chromatography, sequencing and massspectrometry.

In particular, comparison of an unknown protein to polypeptides of knownmolecular weight allows a determination of the apparent molecular weightof the unknown protein (T. D. Brock and M. T. Madigan, Biology ofMicroorganisms 76-77 (Prentice Hall, 6d ed. 1991)). Protein molecularweight standards are commercially available to assist in the estimationof molecular weights of unknown protein (New England Biolabs Inc.Catalog:130-131, 1995; J. L. Hartley, U.S. Pat. No. 5,449,758). However,the molecular weight standards may not correspond closely enough in sizeto the unknown protein to allow an accurate estimation of apparentmolecular weight. The difficulty in estimation of molecular weight iscompounded in the case of proteins that are subjected to fragmentationby chemical or enzymatic means, modified by post-translationalmodification or processing, and/or associated with other proteins innon-covalent complexes.

In addition, the unique nature of the composition of a protein withregard to its specific amino acid constituents results in uniquepositioning of cleavage sites within the protein. Specific fragmentationof a protein by chemical or enzymatic cleavage results in a unique“peptide fingerprint” (D. W. Cleveland et al., J. Biol. Chem.252:1102-1106, 1977; M. Brown et al., J. Gen. Virol. 50:309-316, 1980).Consequently, cleavage at specific sites results in reproduciblefragmentation of a given protein into peptides of precise molecularweights. Furthermore, these peptides possess unique chargecharacteristics that determine the isoelectric pH of the peptide. Theseunique characteristics can be exploited using a variety ofelectrophoretic and other techniques (T. D. Brock and M. T. Madigan,Biology of Microorganisms 76-77 (Prentice Hall, 6d ed. 1991)).

Fragmentation of proteins is further employed for amino acid compositionanalysis and protein sequencing (P. Matsudiara, J. Biol. Chem.262:10035-10038, 1987; C. Eckerskorn et al., Electrophoresis 1988,9:830-838, 1988), particularly the production of fragments from proteinswith a “blocked” N-terminus. In addition, fragmented proteins can beused for immunization, for affinity selection (R. A. Brown, U.S. Pat.No. 5,151,412), for determination of modification sites (e.g.phosphorylation), for generation of active biological compounds (T. D.Brock and M. T. Madigan, Biology of Microorganisms 300-301 (PrenticeHall, 6d ed. 1991)), and for differentiation of homologous proteins (M.Brown et al., J. Gen. Virol. 50:309-316, 1980).

In addition, when a peptide fingerprint of an unknown protein isobtained, it can be compared to a database of known proteins to assistin the identification of the unknown protein using mass spectrometry (W.J. Henzel et al., Proc. Natl. Acad. Sci. USA 90:5011-5015, 1993; D.Fenyo et al., Electrophoresis 19:998-1005, 1998). A variety of computersoftware programs to facilitate these comparisons are accessible via theInternet, such as Protein Prospector (Internet site:prospector.uscf.edu), Multiudent (Internet site:www.expasy.ch/sprot/multiident.html), PeptideSearch (Internet site:www.mann.embl-heiedelberg.de . . . deSearch/FR_PeptideSearch Form.html),and ProFound (Internet site:www.chait-sgi.rockefeller.edu/cgi-bin/prot-id-frag.html). These programsallow the user to specify the cleavage agent and the molecular weightsof the fragmented peptides within a designated tolerance. The programscompare these molecular weights to protein molecular weight informationstored in databases to assist in determining the identity of the unknownprotein. Accurate information concerning the number of fragmentedpeptides and the precise molecular weight of those peptides is requiredfor accurate identification. Therefore, increasing the accuracy indetermining the number of fragmented peptides and their molecular weightshould result in enhanced likelihood of success in the identification ofunknown proteins.

In addition, peptide digests of unknown proteins can be sequenced usingtandem mass spectrometry (MS/MS) and the resulting sequence searchedagainst databases (J. K. Eng, et al., J. Am. Soc. Mass Spec. 5:976-989(1994); M. Mann and M. Wilm, Anal. Chem. 66:4390-4399 (1994); J. A.Taylor and R. S. Johnson, Rapid Comm. Mass Spec. 11:1067-1075 (1997)).Searching programs that can be used in this process exist on theInternet, such as Lutefisk 97 (Internet site:www.lsbc.com:70/Lutefisk97.html), and the Protein Prospector, PeptideSearch and ProFound programs described above. Therefore, adding thesequence of a gene and its predicted protein sequence and peptidefragments to a sequence database can aid in the identification ofunknown proteins using tandem mass spectrometry.

Thus, there also exists a need in the art for polypeptides suitable foruse in peptide fragmentation studies, for use in molecular weightmeasurements, and for use in protein sequencing using tandem massspectrometry.

SUMMARY OF THE INVENTION

The present invention provides isolated nucleic acids and polypeptidesencoded by the nucleic acids for an IL-1 family ligand termed “IL-1zeta” and three splice variants of IL-1 zeta, termed TDZ.1, TDZ.2, andTDZ.3. The present invention also provides isolated nucleic acidmolecules and polypeptides encoded by the nucleic acid molecules for anIL-1 family receptor termed “Xrec2.” Thus, in one aspect, the inventionis directed to isolated nucleic acid molecules of IL-1 zeta, TDZ.1,TDZ.2, and TDZ.3 comprising the DNA sequence of SEQ ID NO: 1, SEQ IDNO:5, SEQ ID NO:6, and SEQ ID NO:7, respectively, and nucleic acidmolecules complementary to SEQ ID NO: 1, 5, 6, and 7. Similarly, theinvention is directed to isolated nucleic acid molecules of Xrec2comprising the nucleic acid molecule of SEQ ID NO:2 and nucleic acidmolecules complementary to SEQ ID NO:2. In another aspect, the inventionis directed to isolated IL-1 zeta, TDZ.1, TDZ.2, and TDZ.3 polypeptideshaving the amino acid sequences SEQ ID NO:3 SEQ ID NO:8, SEQ ID NO:9,and SEQ ID NO:10, respectively, and nucleic acid molecules encoding thepolypeptides of SEQ ID NO:3, 8, 9, and 10. Further included in theinvention are isolated Xrec2 polypeptides comprising the amino acidsequence of SEQ ID NO:4 and nucleic acid molecules that encode thepolypeptide of SEQ ID NO:4

Both single-stranded and double-stranded RNA and DNA nucleic acidmolecules are encompassed by the invention, as well as nucleic acidmolecules that hybridize to a denatured, double-stranded DNA comprisingall or a portion of SEQ ID NOs:1, 2, 5, 6, and 7 and/or a DNA thatencodes the amino acid sequences set forth in SEQ ID NOs:3, 4, 8, 9, and10. Also encompassed are isolated nucleic acid molecules that arederived by in vitro mutagenesis of nucleic acid molecules comprisingsequences of SEQ ID NOs:1, 2, 5, 6, and 7 that are degenerate fromnucleic acid molecules comprising sequences of SEQ ID NOs:1, 2, 5, 6,and 7, and that are allelic variants of DNA of the invention. Theinvention also encompasses recombinant vectors that direct theexpression of these nucleic acid molecules and host cells transformed ortransfected with these vectors.

In addition, the invention encompasses methods of using the nucleicacids noted above to identify nucleic acids encoding proteins havingactivities associated with IL-1 family ligands and receptors. Thus, theIL-1 zeta nucleic acid molecules can be used to identify the IL-1 zetareceptor while the Xrec2 nucleic acid molecule can be used to identifythe Xrec2 ligand.

In addition, these nucleic acids can be used to identify the humanchromosomes with which the nucleic acids are associated. Thus, the IL-1zeta, TDZ.1, TDZ.2, and TDZ.3 nucleic acids can be used to identifyhuman chromosome 2 while the Xrec2 nucleic acids can be used to identifyhuman chromosome X. Accordingly, these nucleic acids can also be used tomap genes on human chromosomes 2 and X, respectively; to identify genesassociated with certain diseases, syndromes, or other human conditionsassociated with human chromosomes 2 and X, respectively; and to studycell signal transduction and the immune system.

The invention also encompasses the use of sense or antisenseoligonucleotides from the nucleic acids of SEQ ID NOs:1, 2, 5, 6, and 7to inhibit the expression of the respective polynucleotide encoded bythe genes of the invention.

The invention also encompasses isolated polypeptides and fragments ofIL-1 zeta and Xrec2 as encoded by these nucleic acid molecules,including soluble polypeptide portions of SEQ ID NOs:3 4, 8, 9, and 10,respectively. The invention further encompasses methods for theproduction of these polypeptides, including culturing a host cell underconditions promoting expression and recovering the polypeptide from theculture medium. Especially, the expression of these polypeptides inbacteria, yeast, plant, insect, and animal cells is encompassed by theinvention.

In general, the polypeptides of the invention can be used to studycellular processes such as immune regulation, cell proliferation, celldeath, cell migration, cell-to-cell interaction, and inflammatoryresponses. In addition, these polypeptides can be used to identifyproteins associated with IL-1 zeta, TDZ.1, TDZ.2, and TDZ.3 ligands andwith Xrec2 receptors.

In addition, the invention includes assays utilizing these polypeptidesto screen for potential inhibitors or enhancers of activity associatedwith the polypeptides of this invention. The present invention alsoincludes assays and screening methods for identifying inhibitors orenhancers of activities associated with counter-structure molecules ofthe polypeptides of this invention. Further, methods of using thesepolypeptides in the design of inhibitors (e.g., engineered receptorsthat act as inhibitors) thereof are also an aspect of the invention.

The present invention further encompasses therapeutic methods utilizingantagonist and/or agonists of the polypeptides of this invention andantagonists or agonists discovered in accordance with the screeningmethods of this invention. For example, IL-1 zeta polypeptides of thepresent invention enhance the secretion of IL-12 from isolated primaryhuman monocytes. In view of IL-12 activity associated with stimulatingand enhancing immune responses and IL-12 activity in promoting Th1mediated diseases, IL-1 zeta polypeptide agonists, together with IL-1zeta antagonists are useful for treating disease or medical conditionsassociated with immune system imbalances, particularly imbalancesinvolving cell-mediated immune responses. For example, inhibitors orantagonists of IL-1 zeta polypeptides can be used to treat diseaseassociated with abnormal Th1 immune responses, including the deleteriouseffects of inflammation. Agonists of IL-1 zeta polypeptide activity areuseful in treating disease responsive to IL-12 stimulation such ascertain infectious diseases, including Leishmania, parasitic diseasesand diseases preferentially inhibited by a Th1 immune response.Additionally 1′-1 zeta polypeptides upregulate TNF expression and thusantagonists of IL-1 zeta polypeptides are useful in treatinginflammatory conditions including rheumatoid arthritis, SLE, myastheniagravis, insulin-dependent diabetes mellitus, thyroiditis, etc. anddiseases preferentially inhibited by a Th1 immune response.

The invention further provides a method for using these polypeptides asmolecular weight markers that allow the estimation of the molecularweight of a protein or a fragmented protein, as well as a method for thevisualization of the molecular weight markers of the invention thereofusing electrophoresis. The invention further encompasses methods forusing the polypeptides of the invention as markers for determining theisoelectric point of an unknown protein, as well as controls forestablishing the extent of fragmentation of a protein.

Further encompassed by this invention are kits to aid in thesedeterminations.

Further encompassed by this invention is the use of the IL-1 zeta andXrec2 nucleic acid sequences, predicted amino acid sequences of thepolypeptide or fragments thereof, or a combination of the predictedamino acid sequences of the polypeptide and fragments thereof for use insearching an electronic database to aid in the identification of samplenucleic acids and/or proteins.

Isolated polyclonal or monoclonal antibodies that bind to thesepolypeptides are also encompassed by the invention, in addition the useof these antibodies to aid in purifying the polypeptides of theinvention.

BRIEF DESCRIPTION OF THE FIGURE

FIG. 1 diagrams the genomic structure of the IL-1 zeta locus.

DETAILED DESCRIPTION OF THE INVENTION

The nucleic acid molecules encompassed in the invention include thefollowing nucleotide sequences: Name: IL-1 zeta 1 ATGTCAGGCT GTGATAGGAGGGAAACAGAA ACCAAAGGAA AGAACAGCTT (SEQ ID NO:1) 51 TAAGAAGCGC TTAAGAGGTCCAAAGGTGAA GAACTTAAAC CCGAAGAAAT 101 TCAGCATTCA TGACCAGGAT CACAAAGTACTGGTCCTGGA CTCTGGGAAT 151 CTCATAGCAG TTCCAGATAA AAACTACATA CGCCCAGAGATCTTCTTTGC 201 ATTAGCCTCA TCCTTGAGCT CAGCCTCTGC GGAGAAAGGA AGTCCGATTC251 TCCTGGGGGT CTCTAAAGGG GAGTTTTGTC TCTACTGTGA CAAGGATAAA 301GGACAAAGTC ATCCATCCCT TCAGCTGAAG AAGGAGAAAC TGATGAAGCT 351 GGCTGCCCAAAAGGAATCAG CACGCCGGCC CTTCATCTTT TATAGGGCTC 401 AGGTGGGCTC CTGGAACATGCTGGAGTCGG CGGCTCACCC CGGATGGTTC 451 ATCTGCACCT CCTGCAATTG TAATGAGCCTGTTGGGGTGA CAGATAAATT 501 TGAGAACAGG AAACACATTG AATTTTCATT TCAACCAGTTTGCAAAGCTG 551 AAATGAGCCC CAGTGAGGTC AGCGATTAG Name: Xrec2 1 ATGAAAGCTCCGATTCCACA CTTGATTCTC TTATACGCTA CTTTTACTCA (SEQ ID NO:2) 51 GAGTTTGAAGGTTGTGACCA AAAGAGGCTC CGCCGATGGA TGCACTGACT 101 GGTCTATCGA TATCAAGAAATATCAAGTTT TGGTGGGAGA GCCTGTTCGA 151 ATCAAATGTG CACTCTTTTA TGGTTATATCAGAACAAATT ACTCCCTTGC 201 CCAAAGTGCT GGACTCAGTT TGATGTGGTA CAAAAGTTCTGGTCCTGGAG 251 ACTTTGAAGA GCCAATAGCC TTTGACGGAA GTAGAATGAG CAAAGAAGAA301 GACTCCATTT GGTTCCGGCC AACATTGCTA CAGGACAGTG GTCTCTACGC 351CTGTGTCATC AGAAACTCCA CTTACTGTAT GAAAGTATCC ATCTCACTGA 401 CAGTGGGTGAAAATGACACT GGACTCTGCT ATAATTCCAA GATGAAGTAT 451 TTTGAAAAAG CTGAACTTAGCAAAAGCAAG GAAATTTCAT GCCGTGACAT 501 AGAGGATTTT CTACTGCCAA CCAGAGAACCTGAAATCCTT TGGTACAAGG 551 AATGCAGGAC AAAAACATGG AGGCCAAGTA TTGTATTCAAAAGAGATACT 601 CTGCTTATAA GAGAAGTCAG AGAAGATGAC ATTGGAAATT ATACCTGTGA651 ATTAAAATAT GGAGGCTTTG TTGTGAGAAG AACTACTGAA TTAACTGTTA 701CAGCCCCTCT GACTGATAAG CCACCCAAGC TTTTGTATCC TATGGAAAGT 751 AAACTGACAATTCAGGAGAC CCAGCTGGGT GACTCTGCTA ATCTAACCTG 801 CAGAGCTTTC TTTGGGTACAGCGGAGATGT CAGTCCTTTA ATTTACTGGA 851 TGAAAGGAGA AAAATTTATT GAAGATCTGGATGAAAATCG AGTTTGGGAA 901 AGTGACATTA GAATTCTTAA GGAGCATCTT GGGGAACAGGAAGTTTCCAT 951 CTCATTAATT GTGGACTCTG TGGAAGAAGG TGACTTGGGA AATTACTCCT1001 GTTATGTTGA AAATGGAAAT GGACGTCGAC ACGCCAGCGT TCTCCTTCAT 1051AAACGAGAGC TAATGTACAC AGTGGAACTT GCTGGAGGCC TTGGTGCTAT 1101 ACTCTTGCTGCTTGTATGTT TGGTGACCAT CTACAAGTGT TACAAGATAG 1151 AAATCATGCT CTTCTACAGGAATCATTTTG GAGCTGAAGA GCTCGATGGA 1201 GACAATAAAG ATTATGATGC ATACTTATCATACACCAAAG TGGATCCTGA 1251 CCAGTGGAAT CAAGAGACTG GGGAAGAAGA ACGTTTTGCCCTTGAAATCC 1301 TACCTGATAT GCTTGAAAAG CATTATGGAT ATAAGTTGTT TATACCAGAT1351 AGAGATTTAA TCCCAACTGG AACATACATT GAAGATGTGG CAAGATGTGT 1401AGATCAAAGC AAGCGGCTGA TTATTGTCAT GACCCCAAAT TACGTAGTTA 1451 GAAGGGGCTGGAGCATCTTT GAGCTGGAAA CCAGACTTCG AAATATGCTT 1501 GTGACTGGAG AAATTAAAGTGATTCTAATT GAATGCAGTG AACTGAGAGG 1551 AATTATGAAC TACCAGGAGG TGGAGGCCCTGAAGCACACC ATCAAGCTCC 1601 TGACGGTCAT TAAATGGCAT GGACCAAAAT GCAACAAGTTGAACTCCAAG 1651 TTCTGGAAAC GTTTACAGTA TGAAATGCCT TTTAAGAGGA TAGAACCCAT1701 TACACATGAG CAGGCTTTAG ATGTCAGTGA GCAAGGGCCT TTTGGGGAGC 1751TGCAGACTGT CTCGGCCATT TCCATGGCCG CGGCCACCTC CACAGCTCTA 1801 GCCACTGCCCATCCAGATCT CCGTTCTACC TTTCACAACA CGTACCATTC 1851 ACAAATGCGT CAGAAACACTACTACCGAAG CTATGAGTAC GACGTACCTC 1901 CTACCGGCAC CCTGCCTCTT ACCTCCATAGGCAATCAGCA TACCTACTGT 1951 AACATCCCTA TGACACTCAT CAACGGGCAG CGGCCACAGACAAAATCGAG 2001 CAGGGAGCAG AATCCAGATG AGGCCCACAC AAACAGTGCC ATCCTGCCGC2051 TGTTGCCAAG GGAGACCAGT ATATCCAGTG TGATATGGTG A Name: TDZ.1 1ATGTCCTTTG TGGGGGAGAA CTCAGGAGTG AAAATGGGCT CTGAGCACTG (SEQ ID NO:5) 51GGAAAAAGAT GAACCCCAGT GCTGCTTAGA AGACCCGGCT GTAAGCCCCC 101 TGGAACCAGGCCCAAGCCTC CCCACCATGA ATTTTGTTCA CACAAGTCCA 151 AAGGTGAAGA ACTTAAACCCGAAGAAATTC AGCATTCATG ACCAGGATCA 201 CAAAGTACTG GTCCTGGACT CTGGGAATCTCATAGCAGTT CCAGATAAAA 251 ACTACATACG CCCAGAGATC TTCTTTGCAT TAGCCTCATCCTTGAGCTCA 301 GCCTCTGCGG AGAAAGGAAG TCCGATTCTC CTGGGGGTCT CTAAACGGGA351 GTTTTGTCTC TACTGTGACA AGGATAAAGG ACAAAGTCAT CCATCCCTTC 401AGCTGAAGAA GGAGAAACTG ATGAAGCTGG CTGCCCAAAA GGAATCAGCA 451 CGCCGGCCCTTCATCTTTTA TAGGGCTCAG GTGGGCTCCT GGAACATGCT 501 GGAGTCGGCG GCTCACCCCGGATGGTTCAT CTGCACCTCC TGCAATTGTA 551 ATGAGCCTGT TGGGGTGACA GATAAATTTGAGAACAGGAA ACACATTGAA 601 TTTTCATTTC AACCAGTTTG CAAAGCTGAA ATGAGCCCCAGTGAGGTCAG 651 CGATTAG Name: TDZ.2 1 ATGTCCTTTG TGGGGGAGAA CTCAGGAGTGAAAATGGGCT CTGAGGACTG (SEQ ID NO:6) 51 GGAAAAAGAT GAACCCCAGT GCTGCTTAGAAGGTCCAAAG GTGAAGAACT 101 TAAACCCGAA GAAATTCAGC ATTCATGACC AGGATCACAAAGTACTGGTC 151 CTGGACTCTG GGAATCTCAT AGCAGTTCCA GATAAAAACT ACATACGCCC201 AGAGATCTTC TTTGCATTAG CCTCATCCTT GAGCTCAGCC TCTGCGGAGA 251AAGGAAGTCC GATTCTCCTG GGGGTCTCTA AAGGGGAGTT TTGTCTCTAC 301 TGTGACAAGGATAAAGGACA AAGTCATCCA TCCCTTCAGC TGAAGAAGGA 351 GAAACTGATG AAGCTGGCTGCCCAAAAGGA ATCAGCACGC CGGCCCTTCA 401 TCTTTTATAG GGCTCAGGTG GGCTCCTGGAACATGCTGGA GTCGGCGGCT 451 CACCCCGGAT GGTTCATCTG CACCTCCTGC AATTGTAATGAGCCTGTTGG 501 GGTGACAGAT AAATTTGAGA ACAGGAAACA CATTGAATTT TCATTTCAAC551 CAGTTTGCAA AGCTGAAATG AGCCCCAGTG AGGTCAGCGA TTAG Name: TDZ.3 1ATGTCCTTTG TGGGGGAGAA CTCAGGAGTG AAAATGGGCT CTGAGGACTG (SEQ ID NO:7) 51GGAAAAAGAT GAACCCCAGT GCTGCTTAGA AGAGATCTTC TTTGCATTAG 101 CCTCATCCTTGAGCTCAGCC TCTGCGGAGA AAGGAAGTCC GATTCTCCTG 151 GGGGTCTCTA AAGGGGAGTTTTGTCTCTAC TGTGACAAGG ATAAAGGACA 201 AAGTCATCCA TCCCTTCAGC TGAAGAAGGAGAAACTGATG AAGCTGGCTG 251 CCCAAAAGGA ATCAGCACGC CGGCCCTTCA TCTTTTATAGGGCTCAGGTG 301 GGCTCCTGGA ACATGCTGGA GTCGGCGGCT CACCCCGGAT GGTTCATCTG351 CACCTCCTGC AATTGTAATG AGCCTGTTGG GGTGACAGAT AAATTTGAGA 401ACAGGAAACA CATTGAATTT TCATTTCAAC CAGTTTGCAA AGCTGAAATG 451 AGCCCCAGTGAGGTCAGCGA TTAG

The amino acid sequences of the polypeptides encoded by the nucleotidesequence of the invention include: Name: IL-1 zeta (polypeptide) 1MSGCDRRETE TKGKNSFKKR LRGPKVKNLN PKKFSIHDQD HKVLVLDSGN (SEQ ID NO:3) 51LIAVPDKNYI RPEIFFALAS SLSSASAEKG SPILLGVSKG EFCLYCDKDK 101 GQSHPSLQLKKEKLMKLAAQ KESARRPFIF YRAQVGSWNM LESAAHPGWF 151 ICTSCNCNEP VGVTDKFENRKHIEFSFQPV CKAEMSPSEV SD* Name: Xrec2 (polypeptide) 1 MKAPIPHLILLYATFTQSLK VVTKRGSADG CTDWSIDIKK YQVLVGEPVR (SEQ ID NO:4) 51 IKCALFYGYIRTNYSLAQSA GLSLMWYKSS GPGDFEEPIA FDGSRMSKEE 101 DSIWFRPTLL QDSGLYACVIRNSTYCMKVS ISLTVGENDT GLCYNSKMKY 151 FEKAELSKSK EISCRDIEDF LLPTREPEILWYKECRTKTW RPSIVFKRDT 201 LLIREVREDD IGNYTCELKY GGFVVRRTTE LTVTAPLTDKPPKLLYPMES 251 KLTIQETQLG DSANLTCRAF FGYSGDVSPL IYWMKGEKFI EDLDENRVWE301 SDIRILKEHL GEQEVSISLI VDSVEEGDLG NYSCYVENGN GRRHASVLLH 351KRELMYTVEL AGGLGAILLL LVCLVTIYKC YKIEIMLFYR NHFGAEELDG 401 DNKDYDAYLSYTKVDPDQWN QETGEEERFA LEILPDMLEK HYGYKLFIPD 451 RDLIPTGTYI EDVARCVDQSKRLIIVMTPN YVVRRGWSIF ELETRLRNML 501 VTGEIKVILI ECSELRGIMN YQEVEALKHTIKLLTVIKWH GPKCNKLNSK 551 FWKRLQYEMP FKRIEPITHE QALDVSEQGP FGELQTVSAISMAAATSTAL 601 ATAHPDLRST FHNTYHSQMR QKHYYRSYEY DVPPTGTLPL TSIGNQHTYC651 NIPMTLINGQ RPQTKSSREQ NPDEAHTNSA ILPLLPRETS ISSVIW* TDZ.1polypeptide 1 MSFVGENSGV KMGSEDWEKD EPQCCLEDPA VSPLEPGPSL PTMNFVHTSP(SEQ ID NO:8) 51 KVKNLNPKKF SIHDQDHKVL VLDSGNLIAV PDKNYIRPEI FFALASSLSS101 ASAEKGSPIL LGVSKGEFCL YCDKDKGQSH PSLQLKKEKL MKLAAQKESA 151RRPFIFYRAQ VGSWNMLESA AHPGWFICTS CNCNEPVGVT DKFENRKHIE 201 FSFQPVCKAEMSPSEVSD* Name: TDZ.2 polypeptide 1 MSFVGENSGV KMGSEDWEKD EPQCCLEGPKVKNLNPKKFS IHDQDHKVLV (SEQ ID NO:9) 51 LDSGNLIAVP DKNYIRPEIF FALASSLSSASAEKGSPILL GVSKGEFCLY 101 CDKDKGQSHP SLQLKKEKLM KLAAQKESAR RPFIFYRAQVGSWNMLESAA 151 HPGWFICTSC NCNEPVGVTD KFENRKHIEF SFQPVCKAEM SPSEVSD*Name: TDZ.3 polypeptide 1 MSFVGENSGV KMGSEDWEKD EPQCCLEEIF FALASSLSSASAEKGSPILL (SEQ ID NO:10) 51 GVSKGEFCLY CDKDKGQSHP SLQLKKEKLM KLAAQKESARRPFIFYRAQV 101 GSWNMLESAA HPGWFICTSC NCNEPVGVTD KFENRKHIEF SFQPVCKAEM151 SPSEVSD*

The discovery of the IL-1 zeta, the IL-1 zeta splice variants (TDZ.1,TDZ.2, and TDZ.3) and the Xrec2 nucleic acids of the invention enablesthe construction of expression vectors comprising nucleic acid sequencesencoding the respective polypeptides and host cells transfected ortransformed with the expression vectors. The invention also enables theisolation and purification of biologically active IL-1 zeta, the IL-1zeta splice variants, and Xrec2 polypeptides and fragments thereof. Inyet another embodiment, the nucleic acids or oligonucleotides thereofcan be used as probes to identify nucleic acid encoding proteins havingassociated activities. Thus, IL-1 zeta and the IL-1 splice variants canbe used to identify activities associated with IL-1 family ligands andXrec2 can be used to identify activities associated with IL-1 familyreceptors. In addition, the nucleic acids or oligonucleotides thereof ofIL-1 zeta can be used to identify human chromosomes 2 while those ofXrec2 can be used to identify human chromosome X. Similarly, thesenucleic acids or oligonucleotides thereof can be used to map genes onhuman chromosomes 2 and X, respectively, and to identify genesassociated with certain diseases, syndromes or other human conditionsassociated with human chromosomes 2 and X. Thus, the nucleic acids oroligonucleotides thereof of IL-1 zeta, TDZ.1, TDZ.2, and TDZ.3 can beused to identify glaucoma, ectodermal dysplasia, insulin-dependentdiabetes mellitus, wrinkly skin syndrome, T-cell leukemia/lymphoma, andtibial muscular dystrophy while the nucleic acids or oligonucleotidesthereof of Xrec2 can be used to identify retinoschisis, lissencephaly,subcortical laminalheteropia, mental retardation, cowchock syndrome,bazex syndrome, hypertrichosis, lymphoproliferative syndrome,immunodeficiency, Langer mesomelic dysplasia, and leukemia. Finally,single-stranded sense or antisense oligonucleotides from these nucleicacids can be used to inhibit expression of polynucleotides encoded bythe IL-1 zeta and Xrec2 genes, respectively.

Further, the IL-1 zeta, TDZ.1, TDZ.2, TDZ.3 and Xrec2 polypeptides andsoluble fragments thereof can be used to activate and/or inhibit theactivation of vascular endothelial cells and lymphocytes, induce and/orinhibit the induction of local tissue destruction and fever (Janeway etal., 1996), inhibit and/or stimulate macrophages and vascularendothelial cells to produce IL-6, induce and/or inhibit the inductionof prostaglandins, nitric oxide synthetase, and metalloproteinases, andupregulate and/or inhibit the upregulation of molecules on the surfaceof vascular endothelial cells. In addition these polypeptides andfragmented peptides can also be used to induce and/or inhibit theinduction of inflammatory mediators such as transcription factors NF-KBand AP-1, MAP kinases JNK and p38, COX-2, iNOS, and all of theactivities stimulated by these molecules.

In addition, these polypeptides and fragmented peptides can be used asmolecular weight markers and as controls for peptide fragmentation, andthe invention includes the kits comprising these reagents. Finally,these polypeptides and fragments thereof can be used to generateantibodies, and the invention includes the use of such antibodies topurify IL-1 zeta and Xrec2 polypeptides.

Nucleic Acid Molecules

In a particular embodiment, the invention relates to certain isolatednucleotide sequences that are free from contaminating endogenousmaterial. A “nucleotide sequence” refers to a polynucleotide molecule inthe form of a separate fragment or as a component of a larger nucleicacid construct. The nucleic acid molecule has been derived from DNA orRNA isolated at least once in substantially pure form and in a quantityor concentration enabling identification, manipulation, and recovery ofits component nucleotide sequences by standard biochemical methods (suchas those outlined in Sambrook et al., Molecular Cloning: A LaboratoryManual, 2nd sed., Cold Spring Harbor Laboratory, Cold Spring Harbor,N.Y. (1989)). Such sequences are preferably provided and/or constructedin the form of an open reading frame uninterrupted by internalnon-translated sequences, or introns, that are typically present ineukaryotic genes. Sequences of non-translated DNA can be present 5′ or3′ from an open reading frame, where the same do not interfere withmanipulation or expression of the coding region.

Nucleic acid molecules of the invention include DNA in bothsingle-stranded and double-stranded form, as well as the RNA complementthereof. DNA includes, for example, cDNA, genomic DNA, chemicallysynthesized DNA, DNA amplified by PCR, and combinations thereof. GenomicDNA may be isolated by conventional techniques, e.g., using the cDNA ofSEQ ID NOs:1, 2, 5, 6, 7 or a suitable fragment thereof, as a probe.

The DNA molecules of the invention include full length genes as well aspolynucleotides and fragments thereof. The full length gene may includethe N-terminal signal peptide. Other embodiments include DNA encoding asoluble form, e.g., encoding the extracellular domain of the protein,either with or without the signal peptide.

The nucleic acids of the invention are preferentially derived from humansources, but the invention includes those derived from non-humanspecies, as well.

Preferred Sequences

The particularly preferred nucleic acid molecules of the invention arethose shown in SEQ ID NOs:1, 5, 6, 7 for IL-1 zeta, TDZ.1, TDZ.2, andTDZ.3, respectively, and SEQ ID NO:2 for Xrec2. cDNA clones having thenucleic acid sequence of SEQ ID NOs:1 and 2 were isolated as describedin Example 1. The sequences of the amino acids of IL-1 zeta and Xrec2encoded by the DNAs of SEQ ID NOs:1 and 2 are shown in SEQ ID NOs:3 and4, respectively. CDNA clones having the nucleic acid sequence of SEQ IDNOs:5, 6, and 7 were isolated as described in Example 8. The sequencesof the amino acids of TDZ.1, TDZ.2, and TDZ.3 encoded by the DNAs of SEQID NOs:5, 6, and 7 are shown in SEQ ID NOs:8, 9, and 10, respectively.

SEQ ID NOs:1-4 identify the IL-1 zeta of SEQ ID NO:3 as a member of theIL-1 family and the Xrec2 of SEQ ID NO:4 as a member of the IL-1receptor family. The homologies on which this is based is set forth atTable I below: TABLE I Protein Source Percent identity to IL-1 zeta IL-1alpha Human LOW IL-1 beta Human 22% IL-1 delta Human 34% IL-1 epsilonHuman 34% IL-18 Human LOW IL-1ra Human 29% Percent identity to Xrec2TIGIRR (IL-1R family member) Human 63% TIGIRR (IL-1R family member)Murine 61% SIGIRR Human 22% IL-1R-AcP Human 35% IL-1R-AcPL Human 26%IL-1R Human 29% RP1 Human 31% RP2 Human 28% ST2 Human 26%

Percent identity of IL-1 zeta and Xrec2 to human and murine proteins.

As described in Example 8, the IL-1 zeta splice variants were discoveredin a stretch of genomic DNA sequence (X22304.gbn). This genomic sequencealso contains the different IL-1 zeta exons and another splice variantknown as Tango-77 (WO 99/06426). Comparing the cDNA sequences of thecloned IL-1 zeta, TDZ.1, TDZ.2, TDZ.3 and Tango-77 with the genomicsequence provides insight into the generation of the splicing events.FIG. 1 shows the genomic structure of the IL-1 zeta locus and the cDNAgenerated by alternative splicing. The numbered boxes indicateindividual exons 1-6 and the approximate size of the intervening intronsis indicated at the top. The asterisk (*) indicates the presence of astop codon, at the end of the coding sequence (exon 6) or as an in-framestop codon (exon 3). “M” indicates potential initiating methionineoriginating either from exon 1 or exon 3. Tango-77 is the cDNA structuredisclosed in WO 99/06426. A significant feature of IL-1 zeta and itssplice variants is the presence or the absence of exon 4. Exon 4 ispresent in IL-1 zeta, TDZ.1 and TDZ.2. It is not present in Tango-77.The amino acid sequence encoded by exon 4 aligns well with the aminoacid sequences of other IL-1 family members in the first few betastrands of the mature peptides. By contrast, the amino acid sequenceencoded by Tango-77 cDNA and by TDZ.3 cDNA aligns well with other IL-1family members in the regions encoded by exons 5 and 6. Exons 5 and 6align well with amino acid sequences of other IL-1 family members in theC-terminal ⅔ of the mature peptide, but does not align well in theN-terminal ⅓. Thus, the “mature peptide” encoded by IL1zeta, TDZ.1 andTDZ.2 DNAs is likely to represent a functional IL-1 like molecule. Thiscontrasts with the polypeptide encoded by Tango-77 or TDZ.3 DNAS whichare less likely to represent a functional IL-1 like molecule.

It is probable that all of the splice isoforms, except TDZ.3, encodeproforms of an IL-1 like cytokine, since in the N-terminal direction theDNAs extend well beyond the N-terminus of mature IL-1 s. Thisobservation predicts that IL-1 zeta, TDZ.1 and TDZ.2 encode the samemature peptide. In connection with this observation it is thepro-domains (as well as 5′ UTRs) that differs between IL-1 zeta, TDZ.1and TDZ.2.

Table II, which details the tissue distribution of IL-1 zeta, TDZ.1,TDZ.2, TDZ.3 and Tango-77, shows that the expression of Tango-77 is morewidespread than that of IL-1 zeta. Table II also shows that the TDZ.1expression is comparable, and almost entirely overlapping, with that ofTango-77. The tissue distribution data combined with the alignmentinformation of FIG. 1 shows that TDZ.1 is the only member of the splicevariants that aligns well with other IL-1 family members, and iswidespread in its expression. These observations suggest that TDZ.1 maybe the most significant of the splice variants in terms of group interms of relevance to biological responses.

Additional Sequences

Due to the known degeneracy of the genetic code, wherein more than onecodon can encode the same amino acid, a DNA sequence can vary from thatshown in SEQ ID NOs:1, 2, 5, 6, and 7 and still encode a polypeptidehaving the amino acid sequence of SEQ ID NOs:3, 4, 8, 9, and 10,respectively. Such variant DNA sequences can result from silentmutations (e.g., occurring during PCR amplification), or can be theproduct of deliberate mutagenesis of a native sequence.

The invention thus provides isolated DNA sequences encoding polypeptidesof the invention, selected from: (a) DNA comprising the nucleotidesequences of SEQ ID NOs:1, 2; 5, 6, and 7 (b) DNA encoding thepolypeptides of SEQ ID NOs:3, 4; 8, 9, and 10 (c) DNA capable ofhybridization to a DNA of (a) or (b) under conditions of moderatestringency and which encodes polypeptides of the invention; (d) DNAcapable of hybridization to a DNA of (a) or (b) under conditions of highstringency and which encodes polypeptides of the invention, and (e) DNAwhich is degenerate, as a result of the genetic code, to a DNA definedin (a), (b), (c), or (d) and which encode polypeptides of the invention.Of course, polypeptides encoded by such DNA sequences are encompassed bythe invention.

As used herein, conditions of moderate stringency can be readilydetermined by those having ordinary skill in the art based on, forexample, the length of the DNA. The basic conditions are set forth bySambrook et al. Molecular Cloning: A Laboratory Manual, 2 ed. Vol. 1,pp. 1.101-104, Cold Spring Harbor Laboratory Press, (1989), and includeuse of a prewashing solution for the nitrocellulose filters 5×SSC, 0.5%SDS, 1.0 mM EDTA (pH 8.0), hybridization conditions of about 50%formamide, 6×SSC at about 42° C. (or other similar hybridizationsolution, such as Stark's solution, in about 50% formamide at about 42°C.), and washing conditions of about 60° C., 0.5×SSC, 0.1% SDS.Conditions of high stringency can also be readily determined by theskilled artisan based on, for example, the length of the DNA. Generally,such conditions are defined as hybridization conditions as above, andwith washing at approximately 68° C., 0.2×SSC, 0.1% SDS. The skilledartisan will recognize that the temperature and wash solution saltconcentration can be adjusted as necessary according to factors such asthe length of the probe.

Also included as an embodiment of the invention is DNA encodingpolypeptide fragments and polypeptides comprising inactivatedN-glycosylation site(s), inactivated protease processing site(s), orconservative amino acid substitution(s), as described below.

In another embodiment, the nucleic acid molecules of the invention alsocomprise nucleotide sequences that are at least 80% identical to anative sequence. Also contemplated are embodiments in which a nucleicacid molecule comprises a sequence that is at least 90% identical, atleast 95% identical, at least 98% identical, at least 99% identical, orat least 99.9% identical to a native sequence.

The percent identity may be determined by visual inspection andmathematical calculation. Alternatively, the percent identity of twonucleic acid sequences can be determined by comparing sequenceinformation using the GAP computer program, version 6.0 described byDevereux et al. (Nucl. Acids Res. 12:387, 1984) and available from theUniversity of Wisconsin Genetics Computer Group (UWGCG). The preferreddefault parameters for the GAP program include: (1) a unary comparisonmatrix (containing a value of 1 for identities and 0 for non-identities)for nucleotides, and the weighted comparison matrix of Gribskov andBurgess, Nucl. Acids Res. 14:6745, 1986, as described by Schwartz andDayhoff, eds., Atlas of Protein Sequence and Structure, NationalBiomedical Research Foundation, pp. 353-358, 1979; (2) a penalty of 3.0for each gap and an additional 0.10 penalty for each symbol in each gap;and (3) no penalty for end gaps. Other programs used by one skilled inthe art of sequence comparison may also be used.

The invention provides isolated nucleic acids useful in the productionof polypeptides. Such polypeptides may be prepared by any of a number ofconventional techniques. A DNA sequence encoding a polypeptide of theinvention, or desired fragment thereof may be subcloned into anexpression vector for production of the polypeptide or fragment. The DNAsequence advantageously is fused to a sequence encoding a suitableleader or signal peptide. Alternatively, the desired fragment may bechemically synthesized using known techniques. DNA fragments also may beproduced by restriction endonuclease digestion of a full length clonedDNA sequence, and isolated by electrophoresis on agarose gels. Ifnecessary, oligonucleotides that reconstruct the 5′ or 3′ terminus to adesired point may be ligated to a DNA fragment generated by restrictionenzyme digestion. Such oligonucleotides may additionally contain arestriction endonuclease cleavage site upstream of the desired codingsequence, and position an initiation codon (ATG) at the N-terminus ofthe coding sequence.

The well-known polymerase chain reaction (PCR) procedure also may beemployed to isolate and amplify a DNA sequence encoding a desiredprotein fragment. Oligonucleotides that define the desired termini ofthe DNA fragment are employed as 5′ and 3′ primers. The oligonucleotidesmay additionally contain recognition sites for restrictionendonucleases, to facilitate insertion of the amplified DNA fragmentinto an expression vector. PCR techniques are described in Saiki et al.,Science 239:487 (1988); Recombinant DNA Methodology, Wu et al., eds.,Academic Press, Inc., San Diego (1989), pp. 189-196; and PCR Protocols:A Guide to Methods and Applications, Innis et al., eds., Academic Press,Inc. (1990).

Polypeptides and Fragments Thereof

The invention encompasses polypeptides and fragments thereof in variousforms, including those that are naturally occurring or produced throughvarious techniques such as procedures involving recombinant DNAtechnology. Such forms include, but are not limited to, derivatives,variants, and oligomers, as well as fusion proteins or fragmentsthereof.

The polypeptides of the invention include full length proteins encodedby the nucleic acid sequences set forth above. Particularly preferredpolypeptides of IL-1 zeta, TDZ.1, TDZ.2 TDZ.3 and Xrec2 comprise theamino acid sequence of SEQ ID NOs:3, 4,8, 9, and 10 respectively. ForTDZ.1 and TDZ.2 the N-terminus does not encode a classical signalpeptide but the extra length relative to the mature form other familymembers is suggestive that it may act as a prodomain. A predictedcleavage site is the point where the conserved structural portion of theprotein begins. Structural modeling data supports this assumption. ForIL-1 zeta and the TDZ.1 and TDZ.2 variants site is somewhere immediatelyupstream of the last three exons. Thus, the polypeptide of IL-1 zeta, asset forth in SEQ ID NO:3, includes a putative pro-domain that extendsfrom amino acids 1 to x, where x is an integer from 20 to 50. Similarly,TDZ.1 of SEQ ID NO:8 includes a putative prodomain that extends fromamino acids 1 to x′ where x′ is an integer from 40-50 and mostpreferably x′ is about 48. TDZ.2 of SEQ ID NO:9 includes a putativeprodomain that extends from amino acids 1 to x″, where x″ is an integerfrom 25-30 and most preferable x″ is 27.

Unlike IL-1 zeta and its splice variants, the polypeptide of Xrec2, asset forth in SEQ ID NO:4, includes an N-terminal hydrophobic region thatfunctions as a signal peptide, followed by an extracellular domaincomprising amino acids 19 to 359, a transmembrane region comprisingamino acids 360 through 378, and a C-terminal cytoplasmic domaincomprising amino acids 379 to 696. Computer analysis predicts that thesignal peptide corresponds to residues 1 to 19 of SEQ ID NO:4 (althoughthe next most likely computer-predicted signal peptide cleavage sites(in descending order) occur after amino acids 20 and 16 of SEQ IDNO:4.)). Cleavage of the signal peptide thus would yield a matureprotein comprising amino acids 19 through 696 of SEQ ID NO:4.

The skilled artisan will recognize that the above-described boundariesof such regions of the polypeptide are approximate. To illustrate, theboundaries of the transmembrane region (which may be predicted by usingcomputer programs available for that purpose) may differ from thosedescribed above.

The polypeptides of the invention may be membrane bound or they may besecreted and, thus, soluble. Soluble polypeptides are capable of beingsecreted from the cells in which they are expressed. In general, solublepolypeptides may be identified (and distinguished from non-solublemembrane-bound counterparts) by separating intact cells which expressthe desired polypeptide from the culture medium, e.g., bycentrifugation, and assaying the medium (supernatant) for the presenceof the desired polypeptide. The presence of polypeptide in the mediumindicates that the polypeptide was secreted from the cells and thus is asoluble form of the protein.

In one embodiment, the soluble polypeptides and fragments thereofcomprise all or part of the extracellular domain, but lack thetransmembrane region that would cause retention of the polypeptide on acell membrane. A soluble polypeptide may include the cytoplasmic domain,or a portion thereof, as long as the polypeptide is secreted from thecell in which it is produced.

In general, the use of soluble forms is advantageous for certainapplications. Purification of the polypeptides from recombinant hostcells is facilitated, since the soluble polypeptides are secreted fromthe cells. Further, soluble polypeptides are generally more suitable forintravenous administration.

The invention also provides polypeptides and fragments of theextracellular domain that retain a desired biological activity.Particular embodiments are directed to polypeptide fragments of SEQ IDNOs:3, 4, 8, 9, and 10 that retain the ability to bind the nativecognates, substrates, or counter-structure (“binding partner”). Such afragment may be a soluble polypeptide, as described above. In anotherembodiment, the polypeptides and fragments advantageously includeregions that are conserved in the IL-1 ligand and IL-1 receptor familyas described above.

Also provided herein are polypeptide fragments comprising at least 20,or at least 30, contiguous amino acids of the sequences of SEQ ID NOs:34, 8, 9, and 10. In one aspect, fragments derived from the cytoplasmicdomain of Xrec2 of SEQ ID NO:4 find use in studies of signaltransduction, and in regulating cellular processes associated withtransduction of biological signals. Polypeptide fragments also may beemployed as immunogens, in generating antibodies.

Variants

Naturally occurring variants as well as derived variants of thepolypeptides and fragments are provided herein.

Variants may exhibit amino acid sequences that are at least 80%identical. Also contemplated are embodiments in which a polypeptide orfragment comprises an amino acid sequence that is at least 90%identical, at least 95% identical, at least 98% identical, at least 99%identical, or at least 99.9% identical to the preferred polypeptide orfragment thereof. Percent identity may be determined by visualinspection and mathematical calculation. Alternatively, the percentidentity of two protein sequences can be determined by comparingsequence information using the GAP computer program, based on thealgorithm of Needleman and Wunsch (J. Mol. B11. 48:443, 1970) andavailable from the University of Wisconsin Genetics Computer Group(UWGCG). The preferred default parameters for the GAP program include:(1) a scoring matrix, blosum62, as described by Henikoff andHenikoff(Proc. Natl. Acad. Sci. USA 89:10915, 1992); (2) a gap weight of12; (3) a gap length weight of 4; and (4) no penalty for end gaps. Otherprograms used by one skilled in the art of sequence comparison may alsobe used.

The variants of the invention include, for example, those that resultfrom alternate mRNA splicing events or from proteolytic cleavage.Alternate splicing of mRNA may, for example, yield a truncated butbiologically active protein, such as a naturally occurring soluble formof the protein. Variations attributable to proteolysis include, forexample, differences in the N- or C-termini upon expression in differenttypes of host cells, due to proteolytic removal of one or more terminalamino acids from the protein (generally from 1-5 terminal amino acids).Proteins in which differences in amino acid sequence are attributable togenetic polymorphism (allelic variation among individuals producing theprotein) are also contemplated herein.

Additional variants within the scope of the invention includepolypeptides that may be modified to create derivatives thereof byforming covalent or aggregative conjugates with other chemical moieties,such as glycosyl groups, lipids, phosphate, acetyl groups and the like.Covalent derivatives may be prepared by linking the chemical moieties tofunctional groups on amino acid side chains or at the N-terminus orC-terminus of a polypeptide. Conjugates comprising diagnostic(detectable) or therapeutic agents attached thereto are contemplatedherein, as discussed in more detail below.

Other derivatives include covalent or aggregative conjugates of thepolypeptides with other proteins or polypeptides, such as by synthesisin recombinant culture as N-terminal or C-terminal fusions. Examples offusion proteins are discussed below in connection with oligomers.Further, fusion proteins can comprise peptides added to facilitatepurification and identification. Such peptides include, for example,poly-His or the antigenic identification peptides described in U.S. Pat.No. 5,011,912 and in Hopp et al., Bio/Technology 6:1204, 1988. One suchpeptide is the FLAG⁷ peptide, Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys, which ishighly antigenic and provides an epitope reversibly bound by a specificmonoclonal antibody, enabling rapid assay and facile purification ofexpressed recombinant protein. A murine hybridoma designated 4E11produces a monoclonal antibody that binds the FLAG⁷ peptide in thepresence of certain divalent metal cations, as described in U.S. Pat.No. 5,011,912, hereby incorporated by reference. The 4E11 hybridoma cellline has been deposited with the American Type Culture Collection underaccession no. HB 9259. Monoclonal antibodies that bind the FLAG⁷ peptideare available from Eastman Kodak Co., Scientific Imaging SystemsDivision, New Haven, Conn.

Among the variant polypeptides provided herein are variants of nativepolypeptides that retain the native biological activity or thesubstantial equivalent thereof. One example is a variant that binds withessentially the same binding affinity as does the native form. Bindingaffinity can be measured by conventional procedures, e.g., as describedin U.S. Pat. No. 5,512,457 and as set forth below.

Variants include polypeptides that are substantially homologous to thenative form, but which have an amino acid sequence different from thatof the native form because of one or more deletions, insertions orsubstitutions. Particular embodiments include, but are not limited to,polypeptides that comprise from one to ten deletions, insertions orsubstitutions of amino acid residues, when compared to a nativesequence.

A given amino acid may be replaced, for example, by a residue havingsimilar physiochemical characteristics. Examples of such conservativesubstitutions include substitution of one aliphatic residue for another,such as Ile, Val, Leu, or Ala for one another; substitutions of onepolar residue for another, such as between Lys and Arg, Glu and Asp, orGln and Asn; or substitutions of one aromatic residue for another, suchas Phe, Trp, or Tyr for one another. Other conservative substitutions,e.g., involving substitutions of entire regions having similarhydrophobicity characteristics, are well known.

Similarly, the DNAs of the invention include variants that differ from anative DNA sequence because of one or more deletions, insertions orsubstitutions, but that encode a biologically active polypeptide.

The invention further includes polypeptides of the invention with orwithout associated native-pattern glycosylation. Polypeptides expressedin yeast or mammalian expression systems (e.g., COS-1 or COS-7 cells)can be similar to or significantly different from a native polypeptidein molecular weight and glycosylation pattern, depending upon the choiceof expression system. Expression of polypeptides of the invention inbacterial expression systems, such as E. coli, provides non-glycosylatedmolecules. Further, a given preparation may include multipledifferentially glycosylated species of the protein. Glycosyl groups canbe removed through conventional methods, in particular those utilizingglycopeptidase. In general, glycosylated polypeptides of the inventioncan be incubated with a molar excess of glycopeptidase (BoehringerMannheim).

Correspondingly, similar DNA constructs that encode various additions orsubstitutions of amino acid residues or sequences, or deletions ofterminal or internal residues or sequences are encompassed by theinvention. For example, N-glycosylation sites in the polypeptideextracellular domain can be modified to preclude glycosylation, allowingexpression of a reduced carbohydrate analog in mammalian and yeastexpression systems. N-glycosylation sites in eukaryotic polypeptides arecharacterized by an amino acid triplet Asn-X-Y, wherein X is any aminoacid except Pro and Y is Ser or Thr. Appropriate substitutions,additions, or deletions to the nucleotide sequence encoding thesetriplets will result in prevention of attachment of carbohydrateresidues at the Asn side chain. Alteration of a single nucleotide,chosen so that Asn is replaced by a different amino acid, for example,is sufficient to inactivate an N-glycosylation site. Alternatively, theSer or Thr can by replaced with another amino acid, such as Ala. Knownprocedures for inactivating N-glycosylation sites in proteins includethose described in U.S. Pat. No. 5,071,972 and EP 276,846, herebyincorporated by reference.

In another example of variants, sequences encoding Cys residues that arenot essential for biological activity can be altered to cause the Cysresidues to be deleted or replaced with other amino acids, preventingformation of incorrect intramolecular disulfide bridges upon folding orrenaturation.

Other variants are prepared by modification of adjacent dibasic aminoacid residues, to enhance expression in yeast systems in which KEX2protease activity is present. EP 212,914 discloses the use ofsite-specific mutagenesis to inactivate KEX2 protease processing sitesin a protein. KEX2 protease processing sites are inactivated bydeleting, adding or substituting residues to alter Arg-Arg, Arg-Lys, andLys-Arg pairs to eliminate the occurrence of these adjacent basicresidues. Lys-Lys pairings are considerably less susceptible to KEX2cleavage, and conversion of Arg-Lys or Lys-Arg to Lys-Lys represents aconservative and preferred approach to inactivating KEX2 sites.

Oligomers

Encompassed by the invention are oligomers or fusion proteins thatcontain EL-1 zeta, TDZ.1, TDZ.2, TDZ.3 or Xrec2 polypeptides. When thepolypeptide of the invention is a type I membrane protein, such asXrec2, the fusion partner is linked to the C terminus of the type Imembrane protein. Such oligomers may be in the form of covalently-linkedor non-covalently-linked multimers, including dimers, trimers, or higheroligomers. As noted above, preferred polypeptides are soluble and thusthese oligomers may comprise soluble polypeptides. In one aspect of theinvention, the oligomers maintain the binding ability of the polypeptidecomponents and provide therefor, bivalent, trivalent, etc., bindingsites.

One embodiment of the invention is directed to oligomers comprisingmultiple polypeptides joined via covalent or non-covalent interactionsbetween peptide moieties fused to the polypeptides. Such peptides may bepeptide linkers (spacers), or peptides that have the property ofpromoting oligomerization. Leucine zippers and certain polypeptidesderived from antibodies are among the peptides that can promoteoligomerization of the polypeptides attached thereto, as described inmore detail below.

Immunoglobulin-Based Oligomers

As one alternative, an oligomer is prepared using polypeptides derivedfrom immunoglobulins. Preparation of fusion proteins comprising certainheterologous polypeptides fused to various portions of antibody-derivedpolypeptides (including the Fc domain) has been described, e.g., byAshkenazi et al. (PNAS USA 88:10535, 1991); Byrn et al. (Nature 344:677,1990); and Hollenbaugh and Aruffo (“Construction of ImmunoglobulinFusion Proteins”, in Current Protocols in Immunology, Suppl. 4, pages10.19.1-10.19.11, 1992).

One embodiment of the present invention is directed to a dimercomprising two fusion proteins created by fusing a polypeptide of theinvention to an Fc polypeptide derived from an antibody. A gene fusionencoding the polypeptide/Fc fusion protein is inserted into anappropriate expression vector. Polypeptide/Fc fusion proteins areexpressed in host cells transformed with the recombinant expressionvector, and allowed to assemble much like antibody molecules, whereuponinterchain disulfide bonds form between the Fc moieties to yielddivalent molecules.

The term “Fc polypeptide” as used herein includes native and muteinforms of polypeptides made up of the Fc region of an antibody comprisingany or all of the CH domains of the Fc region. Truncated forms of suchpolypeptides containing the hinge region that promotes dimerization arealso included. Preferred polypeptides comprise an Fc polypeptide derivedfrom a human IgG1 antibody.

One suitable Fc polypeptide, described in PCT application WO 93/10151,hereby incorporated by reference, is a single chain polypeptideextending from the N-terminal hinge region to the native C-terminus ofthe Fc region of a human IgG1 antibody. Another useful Fc polypeptide isthe Fc mutein described in U.S. Pat. No. 5,457,035 and in Baum et al.,(EMBO J. 13:3992-4001, 1994) incorporated herein by reference. The aminoacid sequence of this mutein is identical to that of the native Fcsequence presented in WO 93/10151, except that amino acid 19 has beenchanged from Leu to Ala, amino acid 20 has been changed from Leu to Glu,and amino acid 22 has been changed from Gly to Ala. The mutein exhibitsreduced affinity for Fc receptors.

The above-described fusion proteins comprising Fc moieties (andoligomers formed therefrom) offer the advantage of facile purificationby affinity chromatography over Protein A or Protein G columns.

In other embodiments, the polypeptides of the invention may besubstituted for the variable portion of an antibody heavy or lightchain. If fusion proteins are made with both heavy and light chains ofan antibody, it is possible to form an oligomer with as many as fourpolypeptide extracellular regions.

Peptide-Linker Based Oligomers

Alternatively, the oligomer is a fusion protein comprising multiplepolypeptides, with or without peptide linkers (spacer peptides). Amongthe suitable peptide linkers are those described in U.S. Pat. Nos.4,751,180 and 4,935,233, which are hereby incorporated by reference. ADNA sequence encoding a desired peptide linker may be inserted between,and in the same reading frame as, the DNA sequences of the invention,using any suitable conventional technique. For example, a chemicallysynthesized oligonucleotide encoding the linker may be ligated betweenthe sequences. In particular embodiments, a fusion protein comprisesfrom two to four soluble polypeptides of the invention, separated bypeptide linkers.

Leucine-Zippers

Another method for preparing the oligomers of the invention involves useof a leucine zipper. Leucine zipper domains are peptides that promoteoligomerization of the proteins in which they are found. Leucine zipperswere originally identified in several DNA-binding proteins (Landschulzet al., Science 240:1759, 1988), and have since been found in a varietyof different proteins. Among the known leucine zippers are naturallyoccurring peptides and derivatives thereof that dimerize or trimerize.

The zipper domain (also referred to herein as an oligomerizing, oroligomer-forming, domain) comprises a repetitive heptad repeat, oftenwith four or five leucine residues interspersed with other amino acids.Examples of zipper domains are those found in the yeast transcriptionfactor GCN4 and a heat-stable DNA-binding protein found in rat liver(C/EBP; Landschulz et al., Science 243:1681, 1989). Two nucleartransforming proteins, fos and jun, also exhibit zipper domains, as doesthe gene product of the murine proto-oncogene, c-myc (Landschulz et al.,Science 240:1759, 1988). The products of the nuclear oncogenes fos andjun comprise zipper domains that preferentially form heterodimers(O'Shea et al., Science 245:646, 1989, Turner and Tjian, Science243:1689, 1989). The zipper domain is necessary for biological activity(DNA binding) in these proteins.

The fusogenic proteins of several different viruses, includingparamyxovirus, coronavirus, measles virus and many retroviruses, alsopossess zipper domains (Buckland and Wild, Nature 338:547,1989; Britton,Nature 353:394, 1991; Delwart and Mosialos, AIDS Research and HumanRetroviruses 6:703, 1990). The zipper domains in these fusogenic viralproteins are near the transmembrane region of the proteins; it has beensuggested that the zipper domains could contribute to the oligomericstructure of the fusogenic proteins. Oligomerization of fusogenic viralproteins is involved in fusion pore formation (Spruce et al, Proc. Natl.Acad. Sci. U.S.A. 88:3523, 1991). Zipper domains have also been recentlyreported to play a role in oligomerization of heat-shock transcriptionfactors (Rabindran et al., Science 259:230, 1993).

Zipper domains fold as short, parallel coiled coils. (O'Shea et al.,Science 254:539; 1991) The general architecture of the parallel coiledcoil has been well characterized, with a “knobs-into-holes” packing asproposed by Crick in 1953 (Acta Crystallogr. 6:689). The dimer formed bya zipper domain is stabilized by the heptad repeat, designated(abcdefg)_(n) according to the notation of McLachlan and Stewart (J.Mol. Biol. 98:293; 1975), in which residues a and d are generallyhydrophobic residues, with d being a leucine, which line up on the sameface of a helix. Oppositely-charged residues commonly occur at positionsg and e. Thus, in a parallel coiled coil formed from two helical zipperdomains, the “knobs” formed by the hydrophobic side chains of the firsthelix are packed into the “holes” formed between the side chains of thesecond helix.

The residues at position d (often leucine) contribute large hydrophobicstabilization energies, and are important for oligomer formation(Krystek: et al., Int. J. Peptide Res. 38:229, 1991). Lovejoy et al.(Science 259:1288, 1993) recently reported the synthesis of atriple-stranded α-helical bundle in which the helices run up-up-down.Their studies confirmed that hydrophobic stabilization energy providesthe main driving force for the formation of coiled coils from helicalmonomers. These studies also indicate that electrostatic interactionscontribute to the stoichiometry and geometry of coiled coils. Furtherdiscussion of the structure of leucine zippers is found in Harbury etal. (Science 262:1401, 26 November 1993)

Examples of leucine zipper domains suitable for producing solubleoligomeric proteins are described in PCT application WO 94/10308, andthe leucine zipper derived from lung surfactant protein D (SPD)described in Hoppe et al. (FEBS Letters 344:191, 1994), herebyincorporated by reference. The use of a modified leucine zipper thatallows for stable trimerization of a heterologous protein fused theretois described in Fanslow et al. (Semin. Immunol. 6:267-278, 1994).Recombinant fusion proteins comprising a soluble polypeptide fused to aleucine zipper peptide are expressed in suitable host cells, and thesoluble oligomer that forms is recovered from the culture supernatant.

Certain leucine zipper moieties preferentially form trimers. One exampleis a leucine zipper derived from lung surfactant protein D (SPD), asdescribed in Hoppe et al. (FEBS Letters 344:191, 1994) and in U.S. Pat.No. 5,716,805, hereby incorporated by reference in their entirety. Thislung SPD-derived leucine zipper peptide comprises the amino acidsequence Pro Asp Val Ala Ser Leu Arg Gln Gln Val Glu Ala Leu Gln Gly GlnVal Gln His Leu Gln Ala Ala Phe Ser Gin Tyr.

Another example of a leucine zipper that promotes trimerization is apeptide comprising the amino acid sequence Arg Met Lys Gln Ile Glu AspLys Ile Glu Glu Ile Leu Ser Lys Ile Tyr His Ile Glu Asn Glu Ile Ala ArgIle Lys Lys Leu Ile Gly Glu Arg, as described in U.S. Pat. No.5,716,805. In one alternative embodiment, an N-terminal Asp residue isadded; in another, the peptide lacks the N-terminal Arg residue.

Fragments of the foregoing zipper peptides that retain the property ofpromoting oligomerization may be employed as well. Examples of suchfragments include, but are not limited to, peptides lacking one or twoof the N-terminal or C-terminal residues presented in the foregoingamino acid sequences. Leucine zippers may be derived from naturallyoccurring leucine zipper peptides, e.g., via conservativesubstitution(s) in the native amino acid sequence, wherein the peptide'sability to promote oligomerization is retained.

Other peptides derived from naturally occurring trimeric proteins may beemployed in preparing trimeric oligomers. Alternatively, syntheticpeptides that promote oligomerization may be employed. In particularembodiments, leucine residues in a leucine zipper moiety are replaced byisoleucine residues. Such peptides comprising isoleucine may be referredto as isoleucine zippers, but are encompassed by the term “leucinezippers” as employed herein.

Production of Polypeptides and Fragments Thereof

Expression, isolation and purification of the polypeptides and fragmentsof the invention may be accomplished by any suitable technique,including but not limited to the following:

Expression Systems

The present invention also provides recombinant cloning and expressionvectors containing DNA, as well as host cell containing the recombinantvectors. Expression vectors comprising DNA may be used to prepare thepolypeptides or fragments of the invention encoded by the DNA. A methodfor producing polypeptides comprises culturing host cells transformedwith a recombinant expression vector encoding the polypeptide, underconditions that promote expression of the polypeptide, then recoveringthe expressed polypeptides from the culture. The skilled artisan willrecognize that the procedure for purifying the expressed polypeptideswill vary according to such factors as the type of host cells employed,and whether the polypeptide is membrane-bound or a soluble form that issecreted from the host cell.

Any suitable expression system may be employed. The vectors include aDNA encoding a polypeptide or fragment of the invention, operably linkedto suitable transcriptional or translational regulatory nucleotidesequences, such as those derived from a mammalian, microbial, viral, orinsect gene. Examples of regulatory sequences include transcriptionalpromoters, operators, or enhancers, an mRNA ribosomal binding site, andappropriate sequences which control transcription and translationinitiation and termination. Nucleotide sequences are operably linkedwhen the regulatory sequence functionally relates to the DNA sequence.Thus, a promoter nucleotide sequence is operably linked to a DNAsequence if the promoter nucleotide sequence controls the transcriptionof the DNA sequence. An origin of replication that confers the abilityto replicate in the desired host cells, and a selection gene by whichtransformants are identified, are generally incorporated into theexpression vector.

In addition, a sequence encoding an appropriate signal peptide (nativeor heterologous) can be incorporated into expression vectors. A DNAsequence for a signal peptide (secretory leader) may be fused in frameto the nucleic acid sequence of the invention so that the DNA isinitially transcribed, and the mRNA translated, into a fusion proteincomprising the signal peptide. A signal peptide that is functional inthe intended host cells promotes extracellular secretion of thepolypeptide. The signal peptide is cleaved from the polypeptide uponsecretion of polypeptide from the cell.

The skilled artisan will also recognize that the position(s) at whichthe signal peptide is cleaved may differ from that predicted by computerprogram, and may vary according to such factors as the type of hostcells employed in expressing a recombinant polypeptide. A proteinpreparation may include a mixture of protein molecules having differentN-terminal amino acids, resulting from cleavage of the signal peptide atmore than one site. Particular embodiments of mature proteins providedherein include, but are not limited to, proteins having the residue atposition 6, 23, 25, 26, 39, 41, or 48 of SEQ ID NO:3 and at position 1or 19 of SEQ ID NO:4 as the N-terminal amino acid.

Suitable host cells for expression of polypeptides include prokaryotes,yeast or higher eukaryotic cells. Mammalian or insect cells aregenerally preferred for use as host cells. Appropriate cloning andexpression vectors for use with bacterial, fungal, yeast, and mammaliancellular hosts are described, for example, in Pouwels et al. CloningVectors: A Laboratory Manual, Elsevier, N.Y., (1985). Cell-freetranslation systems could also be employed to produce polypeptides usingRNAs derived from DNA constructs disclosed herein.

Prokaryotic Systems

Prokaryotes include gram-negative or gram-positive organisms. Suitableprokaryotic host cells for transformation include, for example, E. coli,Bacillus subtilis, Salmonella typhimurium, and various other specieswithin the genera Pseudomonas, Streptomyces, and Staphylococcus. In aprokaryotic host cell, such as E. coli, a polypeptide may include anN-terminal methionine residue to facilitate expression of therecombinant polypeptide in the prokaryotic host cell. The N-terminal Metmay be cleaved from the expressed recombinant polypeptide.

Expression vectors for use in prokaryotic host cells generally compriseone or more phenotypic selectable marker genes. A phenotypic selectablemarker gene is, for example, a gene encoding a protein that confersantibiotic resistance or that supplies an autotrophic requirement.Examples of useful expression vectors for prokaryotic host cells includethose derived from commercially available plasmids such as the cloningvector pBR322 (ATCC 37017). pBR322 contains genes for ampicillin andtetracycline resistance and thus provides simple means for identifyingtransformed cells. An appropriate promoter and a DNA sequence areinserted into the pBR322 vector. Other commercially available vectorsinclude, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala,Sweden) and pGEM1 (Promega Biotec, Madison, Wis., USA).

Promoter sequences commonly used for recombinant prokaryotic host cellexpression vectors include β-lactamase (penicillinase), lactose promotersystem (Chang et al., Nature 275:615, 1978; and Goeddel et al., Nature281:544, 1979), tryptophan (trp) promoter system (Goeddel et al., Nucl.Acids Res. 8:4057, 1980; and EP-A-36776) and tac promoter (Maniatis,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory,p. 412, 1982). A particularly useful prokaryotic host cell expressionsystem employs a phage λP_(L) promoter and a cI857ts thermolabilerepressor sequence. Plasmid vectors available from the American TypeCulture Collection which incorporate derivatives of the λP_(L) promoterinclude plasmid pHUB2 (resident in E. coli strain JMB9, ATCC 37092) andpPLc28 (resident in E. coli RR1, ATCC 53082).

Yeast Systems

Alternatively, the polypeptides may be expressed in yeast host cells,preferably from the Saccharomyces genus (e.g., S. cerevisiae). Othergenera of yeast, such as Pichia or Kluyveromyces, may also be employed.Yeast vectors will often contain an origin of replication sequence froma 2 μ yeast plasmid, an autonomously replicating sequence (ARS), apromoter region, sequences for polyadenylation, sequences fortranscription termination, and a selectable marker gene. Suitablepromoter sequences for yeast vectors include, among others, promotersfor metallothionein, 3-phosphoglycerate kinase (Hitzeman et al., J.Biol. Chem. 255:2073, 1980) or other glycolytic enzymes (Hess et al., J.Adv. Enzyme Reg. 7:149, 1968; and Holland et al., Biochem. 17:4900,1978), such as enolase, glyceraldehyde-3-phosphate dehydrogenase,hexokinase, pyruvate decarboxylase, phosphofructokinase,glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvatekinase, triosephosphate isomerase, phospho-glucose isomerase, andglucokinase. Other suitable vectors and promoters for use in yeastexpression are further described in Hitzeman, EPA-73,657. Anotheralternative is the glucose-repressible ADH2 promoter described byRussell et al. (J. Biol. Chem. 258:2674, 1982) and Beier et al. (Nature300:724, 1982). Shuttle vectors replicable in both yeast and E. coli maybe constructed by inserting DNA sequences from pBR322 for selection andreplication in E. coli (Amp^(r) gene and origin of replication) into theabove-described yeast vectors.

The yeast α-factor leader sequence may be employed to direct secretionof the polypeptide. The α-factor leader sequence is often insertedbetween the promoter sequence and the structural gene sequence. See,e.g., Kurjan et al., Cell 30:933, 1982 and Bitter et al., Proc. Natl.Acad. Sci. USA 81:5330, 1984. Other leader sequences suitable forfacilitating secretion of recombinant polypeptides from yeast hosts areknown to those of skill in the art. A leader sequence may be modifiednear its 3′ end to contain one or more restriction sites. This willfacilitate fusion of the leader sequence to the structural gene.

Yeast transformation protocols are known to those of skill in the art.One such protocol is described by Hinnen et al., Proc. Natl. Acad. Sci.USA 75:1929, 1978. The Hinnen et al. protocol selects for Trp⁺transformants in a selective medium, wherein the selective mediumconsists of 0.67% yeast nitrogen base, 0.5% casamino acids, 2% glucose,10 mg/ml adenine and 20 mg/ml uracil.

Yeast host cells transformed by vectors containing an ADH2 promotersequence may be grown for inducing expression in a “rich” medium. Anexample of a rich medium is one consisting of 1% yeast extract, 2%peptone, and 1% glucose supplemented with 80 mg/ml adenine and 80 mg/mluracil. Derepression of the ADH2 promoter occurs when glucose isexhausted from the medium.

Mammalian or Insect Systems

Mammalian or insect host cell culture systems also may be employed toexpress recombinant polypeptides. Bacculovirus systems for production ofheterologous proteins in insect cells are reviewed by Luckow andSummers, Bio/Technology 6:47 (1988). Established cell lines of mammalianorigin also may be employed. Examples of suitable mammalian host celllines include the COS-7 line of monkey kidney cells (ATCC CRL 1651)(Gluzman et al., Cell 23:175, 1981), L cells, C127 cells, 3T3 cells(ATCC CCL 163), Chinese hamster ovary (CHO) cells, HeLa cells, and BHK(ATCC CRL 10) cell lines, and the CV1/EBNA cell line derived from theAfrican green monkey kidney cell line CV1 (ATCC CCL 70) as described byMcMahan et al. (EMBO J. 10: 2821, 1991).

Established methods for introducing DNA into mammalian cells have beendescribed (Kaufman, R. J., Large Scale Mammalian Cell Culture, 1990, pp.15-69). Additional protocols using commercially available reagents, suchas Lipofectamine lipid reagent (Gibco/BRL) or Lipofectamine-Plus lipidreagent, can be used to transfect cells (Feigner et al., Proc. Natl.Acad. Sci. USA 84:7413-7417, 1987). In addition, electroporation can beused to transfect mammalian cells using conventional procedures, such asthose in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2 ed.Vol. 1-3, Cold Spring Harbor Laboratory Press, 1989). Selection ofstable transformants can be performed using methods known in the art,such as, for example, resistance to cytotoxic drugs. Kaufman et al.,Meth. in Enzymology 185:487-511, 1990, describes several selectionschemes, such as dihydrofolate reductase (DHFR) resistance. A suitablehost strain for DHFR selection can be CHO strain DX-B11, which isdeficient in DHFR (Urlaub and Chasin, Proc. Natl. Acad. Sci. USA77:4216-4220, 1980). A plasmid expressing the DHFR cDNA can beintroduced into strain DX-B11, and only cells that contain the plasmidcan grow in the appropriate selective media. Other examples ofselectable markers that can be incorporated into an expression vectorinclude cDNAs conferring resistance to antibiotics, such as G418 andhygromycin B. Cells harboring the vector can be selected on the basis ofresistance to these compounds.

Transcriptional and translational control sequences for mammalian hostcell expression vectors can be excised from viral genomes. Commonly usedpromoter sequences and enhancer sequences are derived from polyomavirus, adenovirus 2, simian virus 40 (SV40), and human cytomegalovirus.DNA sequences derived from the SV40 viral genome, for example, SV40origin, early and late promoter, enhancer, splice, and polyadenylationsites can be used to provide other genetic elements for expression of astructural gene sequence in a mammalian host cell. Viral early and latepromoters are particularly useful because both are easily obtained froma viral genome as a fragment, which can also contain a viral origin ofreplication (Fiers et al., Nature 273:113, 1978; Kaufman, Meth. inEnzymology, 1990). Smaller or larger SV40 fragments can also be used,provided the approximately 250 bp sequence extending from the Hind IIIsite toward the Bgl I site located in the SV40 viral origin ofreplication site is included.

Additional control sequences shown to improve expression of heterologousgenes from mammalian expression vectors include such elements as theexpression augmenting sequence element (EASE) derived from CHO cells(Morris et al., Animal Cell Technology, 1997, pp. 529-534 and PCTApplication WO 97/25420) and the tripartite leader (TPL) and VA geneRNAs from Adenovirus 2 (Gingeras et al., J. Biol. Chem. 257:13475-13491,1982). The internal ribosome entry site (IRES) sequences of viral originallows dicistronic mRNAs to be translated efficiently (Oh and Sarnow,Current Opinion in Genetics and Development 3:295-300, 1993; Ramesh etal., Nucleic Acids Research 24:2697-2700, 1996). Expression of aheterologous cDNA as part of a dicistronic mRNA followed by the gene fora selectable marker (e.g. DHFR) has been shown to improvetransfectability of the host and expression of the heterologous cDNA(Kaufman, Meth. in Enzymology, 1990). Exemplary expression vectors thatemploy dicistronic mRNAs are pTR-DC/GFP described by Mosser et al.,Biotechniques 22:150-161, 1997, and p2A5I described by Morris et al.,Animal Cell Technology, 1997, pp. 529-534.

A useful high expression vector, pCAVNOT, has been described by Mosleyet al., Cell 59:335-348, 1989. Other expression vectors for use inmammalian host cells can be constructed as disclosed by Okayama and Berg(Mol. Cell. Biol. 3:280, 1983). A useful system for stable high levelexpression of mammalian cDNAs in C127 murine mammary epithelial cellscan be constructed substantially as described by Cosman et al. (Mol.Immunol. 23:935, 1986). A useful high expression vector, PMLSV N1/N4,described by Cosman et al., Nature 312:768, 1984, has been deposited asATCC 39890. Additional useful mammalian expression vectors are describedin EP-A-0367566, and in WO 91/18982, incorporated by reference herein.In yet another alternative, the vectors can be derived fromretroviruses.

Another useful expression vector, pFLAG⁷, can be used. FLAG⁷ technologyis centered on the fusion of a low molecular weight (1 kD), hydrophilic,FLAG⁷ marker peptide to the N-terminus of a recombinant proteinexpressed by pFLAG⁷ expression vectors.

Regarding signal peptides that may be employed, the native signalpeptide may be replaced by a heterologous signal peptide or leadersequence, if desired. The choice of signal peptide or leader may dependon factors such as the type of host cells in which the recombinantpolypeptide is to be produced. To illustrate, examples of heterologoussignal peptides that are functional in mammalian host cells include thesignal sequence for interleukin-7 (IL-7) described in U.S. Pat. No.4,965,195; the signal sequence for interleukin-2 receptor described inCosman et al., Nature 312:768 (1984); the interleukin-4 receptor signalpeptide described in EP 367,566; the type I interleukin-1 receptorsignal peptide described in U.S. Pat. No. 4,968,607; and the type IIinterleukin-1 receptor signal peptide described in EP 460,846.

Purification

The invention also includes methods of isolating and purifying thepolypeptides and fragments thereof.

Isolation and Purification

The “isolated” polypeptides or fragments thereof encompassed by thisinvention are polypeptides or fragments that are not in an environmentidentical to an environment in which it or they can be found in nature.The “purified” polypeptides or fragments thereof encompassed by thisinvention are essentially free of association with other proteins orpolypeptides, for example, as a purification product of recombinantexpression systems such as those described above or as a purifiedproduct from a non-recombinant source such as naturally occurring cellsand/or tissues.

In one preferred embodiment, the purification of recombinantpolypeptides or fragments can be accomplished using fusions ofpolypeptides or fragments of the invention to another polypeptide to aidin the purification of polypeptides or fragments of the invention. Suchfusion partners can include the poly-His or other antigenicidentification peptides described above as well as the Fc moietiesdescribed previously.

With respect to any type of host cell, as is known to the skilledartisan, procedures for purifying a recombinant polypeptide or fragmentwill vary according to such factors as the type of host cells employedand whether or not the recombinant polypeptide or fragment is secretedinto the culture medium.

In general, the recombinant polypeptide or fragment can be isolated fromthe host cells if not secreted, or from the medium or supernatant ifsoluble and secreted, followed by one or more concentration,salting-out, ion exchange, hydrophobic interaction, affinitypurification or size exclusion chromatography steps. As to specific waysto accomplish these steps, the culture medium first can be concentratedusing a commercially available protein concentration filter, forexample, an Amicon or Millipore Pellicon ultrafiltration unit. Followingthe concentration step, the concentrate can be applied to a purificationmatrix such as a gel filtration medium. Alternatively, an anion exchangeresin can be employed, for example, a matrix or substrate having pendantdiethylaminoethyl (DEAE) groups. The matrices can be acrylamide,agarose, dextran, cellulose or other types commonly employed in proteinpurification. Alternatively, a cation exchange step can be employed.Suitable cation exchangers include various insoluble matrices comprisingsulfopropyl or carboxymethyl groups. In addition, a chromatofocusingstep can be employed. Alternatively, a hydrophobic interactionchromatography step can be employed. Suitable matrices can be phenyl oroctyl moieties bound to resins. In addition, affinity chromatographywith a matrix which selectively binds the recombinant protein can beemployed. Examples of such resins employed are lectin columns, dyecolumns, and metal-chelating columns. Finally, one or more reverse-phasehigh performance liquid chromatography (RP-HPLC) steps employinghydrophobic RP-HPLC media, (e.g., silica gel or polymer resin havingpendant methyl, octyl, octyldecyl or other aliphatic groups) can beemployed to further purify the polypeptides. Some or all of theforegoing purification steps, in various combinations, are well knownand can be employed to provide an isolated and purified recombinantprotein.

It is also possible to utilize an affinity column comprising apolypeptide-binding protein of the invention, such as a monoclonalantibody generated against polypeptides of the invention, toaffinity-purify expressed polypeptides. These polypeptides can beremoved from an affinity column using conventional techniques, e.g., ina high salt elution buffer and then dialyzed into a lower salt bufferfor use or by changing pH or other components depending on the affinitymatrix utilized, or be competitively removed using the naturallyoccurring substrate of the affinity moiety, such as a polypeptidederived from the invention.

In this aspect of the invention, polypeptide-binding proteins, such asthe anti-polypeptide antibodies of the invention or other proteins thatmay interact with the polypeptide of the invention, can be bound to asolid phase support such as a column chromatography matrix or a similarsubstrate suitable for identifying, separating, or purifying cells thatexpress polypeptides of the invention on their surface. Adherence ofpolypeptide-binding proteins of the invention to a solid phasecontacting surface can be accomplished by any means. For example,magnetic microspheres can be coated with these polypeptide-bindingproteins and held in the incubation vessel through a magnetic field.Suspensions of cell mixtures are contacted with the solid phase that hassuch polypeptide-binding proteins thereon. Cells having polypeptides ofthe invention on their surface bind to the fixed polypeptide-bindingprotein and unbound cells then are washed away. This affinity-bindingmethod is useful for purifying, screening, or separating suchpolypeptide-expressing cells from solution. Methods of releasingpositively selected cells from the solid phase are known in the art andencompass, for example, the use of enzymes. Such enzymes are preferablynon-toxic and non-injurious to the cells and are preferably directed tocleaving the cell-surface binding partner.

Alternatively, mixtures of cells suspected of containingpolypeptide-expressing cells of the invention first can be incubatedwith a biotinylated polypeptide-binding protein of the invention.Incubation periods are typically at least one hour in duration to ensuresufficient binding to polypeptides of the invention. The resultingmixture then is passed through a column packed with avidin-coated beads,whereby the high affinity of biotin for avidin provides the binding ofthe polypeptide-binding cells to the beads. Use of avidin-coated beadsis known in the art. See Berenson, et al. J. Cell. Biochem., 10D:239(1986). Wash of unbound material and the release of the bound cells isperformed using conventional methods.

The desired degree of purity depends on the intended use of the protein.A relatively high degree of purity is desired when the polypeptide is tobe administered in vivo, for example. In such a case, the polypeptidesare purified such that no protein bands corresponding to other proteinsare detectable upon analysis by SDS-polyacrylamide gel electrophoresis(SDS-PAGE). It will be recognized by one skilled in the pertinent fieldthat multiple bands corresponding to the polypeptide may be visualizedby SDS-PAGE, due to differential glycosylation, differentialpost-translational processing, and the like. Most preferably, thepolypeptide of the invention is purified to substantial homogeneity, asindicated by a single protein band upon analysis by SDS-PAGE. Theprotein band may be visualized by silver staining, Coomassie bluestaining, or (if the protein is radiolabeled) by autoradiography.

Assays

The purified polypeptides of the invention (including proteins,polypeptides, fragments, variants, oligomers, and other forms) may betested for the ability to bind the binding partner in any suitableassay, such as a conventional binding assay. To illustrate, thepolypeptide may be labeled with a detectable reagent (e.g., aradionuclide, chromophore, enzyme that catalyzes a colorimetric orfluorometric reaction, and the like). The labeled polypeptide iscontacted with cells expressing the binding partner. The cells then arewashed to remove unbound labeled polypeptide, and the presence ofcell-bound label is determined by a suitable technique, chosen accordingto the nature of the label.

One example of a binding assay procedure is as follows. A recombinantexpression vector containing the binding partner cDNA is constructedusing methods well known in the art. CV1-EBNA-1 cells in 10 cm² dishesare transfected with the recombinant expression vector. CV-1/EBNA-1cells (ATCC CRL 10478) constitutively express EBV nuclear antigen-1driven from the CMV immediate-early enhancer/promoter. CV1-EBNA-1 wasderived from the African Green Monkey kidney cell line CV-1 (ATCC CCL70), as described by McMahan et al. (EMBO J. 10:2821, 1991).

The transfected cells are cultured for 24 hours, and the cells in eachdish then are split into a 24-well plate. After culturing an additional48 hours, the transfected cells (about 4×10⁴ cells/well) are washed withBM-NFDM, which is binding medium (RPMI 1640 containing 25 mg/ml bovineserum albumin, 2 mg/ml sodium azide, 20 mM Hepes pH 7.2) to which 50mg/ml nonfat dry milk has been added. The cells then are incubated for 1hour at 37° C. with various concentrations of, for example, a solublepolypeptide/Fc fusion protein made as set forth above. Cells then arewashed and incubated with a constant saturating concentration of a¹²⁵I-mouse anti-human IgG in binding medium, with gentle agitation for 1hour at 37° C. After extensive washing, cells are released viatrypsinization.

The mouse anti-human IgG employed above is directed against the Fcregion of human IgG and can be obtained from Jackson ImmunoresearchLaboratories, Inc., West Grove, Pa. The antibody is radioiodinated usingthe standard chloramine-T method. The antibody will bind to the Fcportion of any polypeptide/Fc protein that has bound to the cells. Inall assays, non-specific binding of ¹²⁵I-antibody is assayed in theabsence of the Fc fusion protein/Fc, as well as in the presence of theFc fusion protein and a 200-fold molar excess of unlabeled mouseanti-human IgG antibody.

Cell-bound ¹²⁵I-antibody is quantified on a Packard Autogamma counter.Affinity calculations (Scatchard, Ann. N.Y. Acad. Sci. 51:660, 1949) aregenerated on RS/1 (BBN Software, Boston, Mass.) run on a Microvaxcomputer.

Another type of suitable binding assay is a competitive binding assay.To illustrate, biological activity of a variant may be determined byassaying for the variant's ability to compete with the native proteinfor binding to the binding partner.

Competitive binding assays can be performed by conventional methodology.Reagents that may be employed in competitive binding assays includeradiolabeled polypeptides of the invention and intact cells expressingthe binding partner (endogenous or recombinant). For example, aradiolabeled soluble IL-1 zeta fragment can be used to compete with asoluble IL-1 zeta variant for binding to cell surface IL-1 zetareceptors. Instead of intact cells, one could substitute a solublebinding partner/Fc fusion protein bound to a solid phase through theinteraction of Protein A or Protein G (on the solid phase) with the Fcmoiety. Chromatography columns that contain Protein A and Protein Ginclude those available from Pharmacia Biotech, Inc., Piscataway, N.J.

Another type of competitive binding assay utilizes radiolabeled solublebinding partner, such as a soluble IL-1 zeta receptor/Fc fusion or Xrec2ligand/Fc fusion protein, and intact cells expressing the bindingpartner. Qualitative results can be obtained by competitiveautoradiographic plate binding assays, while Scatchard plots (Scatchard,Ann. N.Y. Acad. Sci. 51:660, 1949) may be utilized to generatequantitative results.

Use of IL-1 ZETA, TDZ.1, TDZ.2, TDZ.3 AND XREC2 Nucleic Acid orOligonucleotides

In addition to being used to express polypeptides as described above,the nucleic acids of the invention, including DNA, and oligonucleotidesthereof can be used:

-   -   as probes to identify nucleic acid encoding proteins of the IL-1        ligand and receptor families;    -   to identify human chromosomes 2 and X;    -   to map genes on human chromosomes 2 and X;    -   to identify genes associated with certain diseases, syndromes,        or other conditions associated with human chromosomes 2 and X;    -   as single-stranded sense or antisense oligonucleotides, to        inhibit expression of polypeptides encoded by the IL-1 zeta,        TDZ.1, TDZ.2, TDZ.3 and Xrec2 genes;    -   to help detect defective genes in an individual; and    -   for gene therapy.

Probes

Among the uses of nucleic acids of the invention is the use of fragmentsas probes or primers. Such fragments generally comprise at least about17 contiguous nucleotides of a DNA sequence. In other embodiments, a DNAfragment comprises at least 30, or at least 60, contiguous nucleotidesof a DNA sequence.

Because homologs of SEQ ID NOs:1, 2, 5, 6 and 7, from other mammalianspecies, are contemplated herein, probes based on the human DNAsequences of SEQ ID NOs:1, 2, 5, 6 and 7 may be used to screen cDNAlibraries derived from other mammalian species, using conventionalcross-species hybridization techniques.

Using knowledge of the genetic code in combination with the amino acidsequences set forth above, sets of degenerate oligonucleotides can beprepared. Such oligonucleotides are useful as primers, e.g., inpolymerase chain reactions (PCR), whereby DNA fragments are isolated andamplified.

Chromosome Mapping

All or a portion of the nucleic acids of IL-1 zeta of SEQ ID NO: 1 andof Xrec2 of SEQ ID NO:2, including oligonucleotides, can be used bythose skilled in the art using well-known techniques to identify thehuman chromosomes 2 and X, respectively, as well as the specific locusthereof, that contains the DNA of IL-1 ligand and IL-1 receptor familymembers. Useful techniques include, but are not limited to, using thesequence or portions, including oligonucleotides, as a probe in variouswell-known techniques such as radiation hybrid mapping (highresolution), in situ hybridization to chromosome spreads (moderateresolution), and Southern blot hybridization to hybrid cell linescontaining individual human chromosomes (low resolution).

For example, chromosomes can be mapped by radiation hybridization. PCRis performed using the Whitehead Institute/MIT Center for GenomeResearch Genebridge4 panel of 93 radiation hybrids(http://www-genome.wi.mit.edu/ftp/distribution/human_STS_releases/july97/rhmap/genebridge4.html).Primers are used which lie within a putative exon of the gene ofinterest and which amplify a product from human genomic DNA, but do notamplify hamster genomic DNA. The results of the PCRs are converted intoa data vector that is submitted to the Whitehead/MIT Radiation Mappingsite on the internet (http://www-seq.wi.mit.edu). The data is scored andthe chromosomal assignment and placement relative to known Sequence TagSite (STS) markers on the radiation hybrid map is provided. Thefollowing web site provides additional information about radiationhybrid mapping:http://www-genome.wi.mit.edu/ftp/distribution/human_STS_releases/july97/07-97.INTRO.html).

Identifying Associated Diseases

As set forth below, IL-1 zeta of SEQ ID NO:1, IL-1 zeta splice variants,and Xrec2 of SEQ ID NO:2 have been mapped by radiation hybridization andhigh-throughput-shotgun sequencing to the 2q11-12 and Xp22 regions ofhuman chromosomes 2 and X, respectively. Human chromosome 2 isassociated with specific diseases which include but are not limited toglaucoma, ectodermal dysplasia, insulin-dependent diabetes mellitus,wrinkly skin syndrome, T-cell leukemia/lymphoma, and tibial musculardystrophy while human chromosome X is associated with retinoschisis,lissencephaly, subcortical laminalheteropia, mental retardation,cowchock syndrome, bazex syndrome, hypertrichosis, lymphoproliferativesyndrome, immunodeficiency, Langer mesomelic dysplasia, and leukemia.Thus, the nucleic acids of SEQ ID NOs:1 and 2 or a fragment thereof canbe used by one skilled in the art using well-known techniques to analyzeabnormalities associated with gene mapping to chromosomes 2 and X. Thisenables one to distinguish conditions in which this marker is rearrangedor deleted. In addition, nucleotides of SEQ ID NOs:1, 2, 5, 6 and 7 or afragment thereof can be used as a positional marker to map other genesof unknown location.

The DNA may be used in developing treatments for any disorder mediated(directly or indirectly) by defective, or insufficient amounts of, thegenes corresponding to the nucleic acids of the invention. Disclosureherein of native nucleotide sequences permits the detection of defectivegenes, and the replacement thereof with normal genes. Defective genesmay be detected in in vitro diagnostic assays, and by comparison of anative nucleotide sequence disclosed herein with that of a gene derivedfrom a person suspected of harboring a defect in this gene.

Sense-Antisense

Other useful fragments of the nucleic acids include antisense or senseoligonucleotides comprising a single-stranded nucleic acid sequence(either RNA or DNA) capable of binding to target mRNA (sense) or DNA(antisense) sequences. Antisense or sense oligonucleotides according tothe present invention comprise a fragment of DNA (SEQ ID NOs:1, 2, 5, 6and 7). Such a fragment generally comprises at least about 14nucleotides, preferably from about 14 to about 30 nucleotides. Theability to derive an antisense or a sense oligonucleotide, based upon acDNA sequence encoding a given protein is described in, for example,Stein and Cohen (Cancer Res. 48:2659, 1988) and van der Krol et al.(BioTechniques 6:958, 1988).

Binding of antisense or sense oligonucleotides to target nucleic acidsequences results in the formation of duplexes that block or inhibitprotein expression by one of several means, including enhanceddegradation of the mRNA by RNAseH, inhibition of splicing, prematuretermination of transcription or translation, or by other means. Theantisense oligonucleotides thus may be used to block expression ofproteins. Antisense or sense oligonucleotides further compriseoligonucleotides having modified sugar-phosphodiester backbones (orother sugar linkages, such as those described in WO91/06629) and whereinsuch sugar linkages are resistant to endogenous nucleases. Sucholigonucleotides with resistant sugar linkages are stable in vivo (i.e.,capable of resisting enzymatic degradation) but retain sequencespecificity to be able to bind to target nucleotide sequences.

Other examples of sense or antisense oligonucleotides include thoseoligonucleotides which are covalently linked to organic moieties, suchas those described in WO 90/10448, and other moieties that increasesaffinity of the oligonucleotide for a target nucleic acid sequence, suchas poly-(L-lysine). Further still, intercalating agents, such asellipticine, and alkylating agents or metal complexes may be attached tosense or antisense oligonucleotides to modify binding specificities ofthe antisense or sense oligonucleotide for the target nucleotidesequence.

Antisense or sense oligonucleotides may be introduced into a cellcontaining the target nucleic acid sequence by any gene transfer method,including, for example, lipofection, CaPO₄-mediated DNA transfection,electroporation, or by using gene transfer vectors such as Epstein-Barrvirus.

Sense or antisense oligonucleotides also may be introduced into a cellcontaining the target nucleotide sequence by formation of a conjugatewith a ligand binding molecule, as described in WO 91/04753. Suitableligand binding molecules include, but are not limited to, cell surfacereceptors, growth factors, other cytokines, or other ligands that bindto cell surface receptors. Preferably, conjugation of the ligand bindingmolecule does not substantially interfere with the ability of the ligandbinding molecule to bind to its corresponding molecule or receptor, orblock entry of the sense or antisense oligonucleotide or its conjugatedversion into the cell.

Alternatively, a sense or an antisense oligonucleotide may be introducedinto a cell containing the target nucleic acid sequence by formation ofan oligonucleotide-lipid complex, as described in WO 90/10448. The senseor antisense oligonucleotide-lipid complex is preferably dissociatedwithin the cell by an endogenous lipase.

IL-1 zeta anti-sense are useful as therapeutics to treat medicalconditions and disease associated with immune system dysfunction andIL-12 production. Such medical conditions and disease are describedbelow and include the deleterious effects of inflammation andauto-immune diseases. Accordingly, IL-1 zeta anti-sense are IL-12antagonists and are useful in treating disease and medical conditionsthat are benefited by IL-12 expression downregulation.

Use of IL-1 ZETA TDZ.1, TDZ.2 TDZ.3 AND XREC2 Polypeptides andFragmented Polypeptides

Uses include, but are not limited to, the following:

-   -   Purifying proteins and measuring activity thereof    -   Delivery Agents    -   Therapeutic and Research Reagents    -   Molecular weight and Isoelectric focusing markers    -   Controls for peptide fragmentation    -   Identification of unknown proteins    -   Preparation of Antibodies

Purification Reagents

Each of the polypeptides of the invention finds use as a proteinpurification reagent. The polypeptides may be attached to a solidsupport material and used to purify the binding partner proteins byaffinity chromatography. In particular embodiments, a polypeptide (inany form described herein that is capable of binding the bindingpartner) is attached to a solid support by conventional procedures. Asone example, chromatography columns containing functional groups thatwill react with functional groups on amino acid side chains of proteinsare available (Pharmacia Biotech, Inc., Piscataway, N.J.). In analternative, a polypeptide/Fc protein (as discussed above) is attachedto Protein A- or Protein G-containing chromatography columns throughinteraction with the Fc moiety.

The polypeptide also finds use in purifying or identifying cells thatexpress the binding partner on the cell surface. Polypeptides are boundto a solid phase such as a column chromatography matrix or a similarsuitable substrate. For example, magnetic microspheres can be coatedwith the polypeptides and held in an incubation vessel through amagnetic field. Suspensions of cell mixtures containing the bindingpartner expressing cells are contacted with the solid phase having thepolypeptides thereon. Cells expressing the binding partner on the cellsurface bind to the fixed polypeptides, and unbound cells then arewashed away.

Alternatively, the polypeptides can be conjugated to a detectablemoiety, then incubated with cells to be tested for binding partnerexpression. After incubation, unbound labeled matter is removed and thepresence or absence of the detectable moiety on the cells is determined.

In a further alternative, mixtures of cells suspected of containingcells expressing the binding partner are incubated with biotinylatedpolypeptides. Incubation periods are typically at least one hour induration to ensure sufficient binding. The resulting mixture then ispassed through a column packed with avidin-coated beads, whereby thehigh affinity of biotin for avidin provides binding of the desired cellsto the beads. Procedures for using avidin-coated beads are known (seeBerenson, et al. J. Cell. Biochem., 10D:239, 1986). Washing to removeunbound material, and the release of the bound cells, are performedusing conventional methods.

Measuring Activity

Polypeptides also find use in measuring the biological activity of thebinding partner protein in terms of their binding affinity. Thepolypeptides thus may be employed by those conducting “qualityassurance” studies, e.g., to monitor shelf life and stability of proteinunder different conditions. For example, the polypeptides may beemployed in a binding affinity study to measure the biological activityof a binding partner protein that has been stored at differenttemperatures, or produced in different cell types. The proteins also maybe used to determine whether biological activity is retained aftermodification of a binding partner protein (e.g., chemical modification,truncation, mutation, etc.). The binding affinity of the modifiedbinding partner protein is compared to that of an unmodified bindingpartner protein to detect any adverse impact of the modifications onbiological activity of the binding partner. The biological activity of abinding partner protein thus can be ascertained before it is used in aresearch study, for example.

Delivery Agents

The polypeptides also find use as carriers for delivering agentsattached thereto to cells bearing the binding partner. The polypeptidesthus can be used to deliver diagnostic or therapeutic agents to suchcells (or to other cell types found to express the binding partner onthe cell surface) in in vitro or in vivo procedures.

Detectable (diagnostic) and therapeutic agents that may be attached to apolypeptide include, but are not limited to, toxins, other cytotoxicagents, drugs, radionuclides, chromophores, enzymes that catalyze acolorimetric or fluorometric reaction, and the like, with the particularagent being chosen according to the intended application. Among thetoxins are ricin, abrin, diphtheria toxin, Pseudomonas aeruginosaexotoxin A, ribosomal inactivating proteins, mycotoxins such astrichothecenes, and derivatives and fragments (e.g., single chains)thereof. Radionuclides suitable for diagnostic use include, but are notlimited to, ¹²³I, ¹³¹I, ^(99m)Tc, ¹¹¹In, and ⁷⁶Br. Examples ofradionuclides suitable for therapeutic use are ¹³¹I, ²¹¹At, ⁷⁷Br, ¹⁸⁶Re,¹⁸⁸Re, ²¹²Pb, ²¹²Bi, ¹⁰⁹Pd, ⁶⁴Cu, and ⁶⁷Cu.

Such agents may be attached to the polypeptide by any suitableconventional procedure. The polypeptide comprises functional groups onamino acid side chains that can be reacted with functional groups on adesired agent to form covalent bonds, for example. Alternatively, theprotein or agent may be derivatized to generate or attach a desiredreactive functional group. The derivatization may involve attachment ofone of the bifunctional coupling reagents available for attachingvarious molecules to proteins (Pierce Chemical Company, Rockford, Ill.).A number of techniques for radiolabeling proteins are known.Radionuclide metals may be attached to polypeptides by using a suitablebifunctional chelating agent, for example.

Conjugates comprising polypeptides and a suitable diagnostic ortherapeutic agent (preferably covalently linked) are thus prepared. Theconjugates are administered or otherwise employed in an amountappropriate for the particular application.

Therapeutic Agents

Polypeptides of the invention may be used in developing treatments forany disorder mediated (directly or indirectly) by defective, orinsufficient amounts of the polypeptides. These polypeptides may beadministered to a mammal afflicted with such a disorder.

The polypeptides may also be employed in inhibiting a biologicalactivity of the binding partner, in in vitro or in vivo procedures. Forexample, a purified Xrec2 receptor polypeptide may be used to inhibitbinding of Xrec2 ligand to endogenous cell surface Xrec2 receptor, or apurified IL-1 zeta polypeptide, or any of its splice variants can beused to inhibit binding of endogenous IL-1 zeta or splice variants toits cell surface receptor. Biological effects that result from thebinding of Xrec2 ligand to endogenous Xrec2 receptors thus areinhibited. In particular, IL-1 zeta polypeptides and fragments of thesepolypeptides that induce IL-12 expression are useful to upregulate IL-12expression in individuals who can benefit from increased IL-12production, including individuals who benefit from enhanced cellmediated immunity. Diseases and medical conditions treatable withagonists of IL-1 zeta polypeptide, as described below, may be suitablytreated using IL-1 zeta polypeptides and fragments of this invention.

Polypeptides of the invention may be administered to a mammal to treat abinding partner-mediated disorder. Such binding partner-mediateddisorders include conditions caused (directly or indirectly) orexacerbated by the binding partner.

Compositions of the present invention may contain a polypeptide in anyform described herein, such as native proteins, variants, derivatives,oligomers, and biologically active fragments. In particular embodiments,the composition comprises a soluble polypeptide or an oligomercomprising soluble polypeptides of the invention.

Compositions comprising an effective amount of a polypeptide of thepresent invention, in combination with other components such as aphysiologically acceptable diluent, carrier, or excipient, are providedherein. The polypeptides can be formulated according to known methodsused to prepare pharmaceutically useful compositions. They can becombined in admixture, either as the sole active material or with otherknown active materials suitable for a given indication, withpharmaceutically acceptable diluents (e.g., saline, Tris-HCl, acetate,and phosphate buffered solutions), preservatives (e.g., thimerosal,benzyl alcohol, parabens), emulsifiers, solubilizers, adjuvants and/orcarriers. Suitable formulations for pharmaceutical compositions includethose described in Remington's Pharmaceutical Sciences, 16th ed. 1980,Mack Publishing Company, Easton, Pa.

In addition, such compositions can be complexed with polyethylene glycol(PEG), metal ions, or incorporated into polymeric compounds such aspolyacetic acid, polyglycolic acid, hydrogels, dextran, etc., orincorporated into liposomes, microemulsions, micelles, unilamellar ormultilamellar vesicles, erythrocyte ghosts or spheroblasts. Suchcompositions will influence the physical state, solubility, stability,rate of in vivo release, and rate of in vivo clearance, and are thuschosen according to the intended application.

The compositions of the invention can be administered in any suitablemanner, e.g., topically, parenterally, or by inhalation. The term“parenteral” includes injection, e.g., by subcutaneous, intravenous, orintramuscular routes, also including localized administration, e.g., ata site of disease or injury. Sustained release from implants is alsocontemplated. One skilled in the pertinent art will recognize thatsuitable dosages will vary, depending upon such factors as the nature ofthe disorder to be treated, the patient's body weight, age, and generalcondition, and the route of administration. Preliminary doses can bedetermined according to animal tests, and the scaling of dosages forhuman administration is performed according to art-accepted practices.

Compositions comprising nucleic acids in physiologically acceptableformulations are also contemplated. DNA may be formulated for injection,for example.

Research Agents

Another use of the polypeptide of the present invention is as a researchtool for studying the biological effects that result from theinteractions of IL-1 zeta, or any of its splice variants, with itsbinding partner, and of Xrec2 with its binding partner, or frominhibiting these interactions, on different cell types. Polypeptidesalso may be employed in in vitro assays for detecting IL-1 zeta, Xrec2,the respective binding partners or the interactions thereof.

Another embodiment of the invention relates to uses of the polypeptidesof the invention to study cell signal transduction. IL-1 family ligandsand receptors play a central role in protection against infection andimmune inflammatory responses which includes cellular signaltransduction, activating vascular endothelial cells and lymphocytes,induction of inflammatory cytokines, acute phase proteins,hematopoiesis, fever, bone resorption, prostaglandins,metalloproteinases, and adhesion molecules. With the continued increasein the number of known IL-1 family members, a suitable classificationscheme is one based on comparing polypeptide structure as well asfunction (activation and regulatory properties). Thus, IL-1 zeta, TDZ.1,TDZ.2, and TDZ.3, like other IL-1 family ligands (IL-1α, IL-1β, andIL-18) and Xrec2, like other IL-1R family receptors (IL-1R1, IL-1R1,IL-1Rrp1, and AcPL), would likely be involved in many of the functionsnoted above as well as promote inflammatory responses and thereforeperhaps be involved in the causation and maintenance of inflammatoryand/or autoimmune diseases such as rheumatoid arthritis, inflammatorybowel disease, and psoriasis. As such, alterations in the expressionand/or activation of the polypeptides of the invention can have profoundeffects on a plethora of cellular processes, including, but not limitedto, activation or inhibition of cell specific responses andproliferation. Expression of cloned IL-1 zeta, Xrec2, or of functionallyinactive mutants thereof can be used to identify the role a particularprotein plays in mediating specific signaling events.

IL-1 mediated cellular signaling often involves a molecular activationcascade, during which a receptor propagates a ligand-receptor mediatedsignal by specifically activating intracellular kinases whichphosphorylate target substrates. These substrates can themselves bekinases which become activated following phosphorylation. Alternatively,they can be adapter molecules that facilitate down stream signalingthrough protein-protein interaction following phosphorylation.Regardless of the nature of the substrate molecule(s), expressedfunctionally active versions of Xrec2, IL-1 zeta, its splice variants,and their binding partners can be used to identify what substrate(s)were recognized and activated by the polypeptides of the invention. Assuch, these novel polypeptides can be used as reagents to identify novelmolecules involved in signal transduction pathways.

Molecular Weight, Isoelectric Point Markers

The polypeptides of the present invention can be subjected tofragmentation into smaller peptides by chemical and enzymatic means, andthe peptide fragments so produced can be used in the analysis of otherproteins or polypeptides. For example, such peptide fragments can beused as peptide molecular weight markers, peptide isoelectric pointmarkers, or in the analysis of the degree of peptide fragmentation.Thus, the invention also includes these polypeptides and peptidefragments, as well as kits to aid in the determination of the apparentmolecular weight and isoelectric point of an unknown protein and kits toassess the degree of fragmentation of an unknown protein.

Although all methods of fragmentation are encompassed by the invention,chemical fragmentation is a preferred embodiment, and includes the useof cyanogen bromide to cleave under neutral or acidic conditions suchthat specific cleavage occurs at methionine residues (E. Gross, Methodsin Enz. 11:238-255, 1967). This can further include additional steps,such as a carboxymethylation step to convert cysteine residues to anunreactive species.

Enzymatic fragmentation is another preferred embodiment, and includesthe use of a protease such as Asparaginylendo-peptidase,Arginylendo-peptidase, Achromobacter protease I, Trypsin, Staphlococcusaureus V8 protease, Endoproteinase Asp-N, or Endoproteinase Lys-C underconventional conditions to result in cleavage at specific amino acidresidues. Asparaginylendo-peptidase can cleave specifically on thecarboxyl side of the asparagine residues present within the polypeptidesof the invention. Arginylendo-peptidase can cleave specifically on thecarboxyl side of the arginine residues present within thesepolypeptides. Achromobacter protease I can cleave specifically on thecarboxyl side of the lysine residues present within the polypeptides(Sakiyama and Nakat, U.S. Pat. No. 5,248,599; T. Masaki et al., Biochim.Biophys. Acta 660:44-50, 1981; T. Masaki et al., Biochim. Biophys. Acta660:51-55, 1981). Trypsin can cleave specifically on the carboxyl sideof the arginine and lysine residues present within polypeptides of theinvention. Enzymatic fragmentation may also occur with a protease thatcleaves at multiple amino acid residues. For example, Staphlococcusaureus V8 protease can cleave specifically on the carboxyl side of theaspartic and glutamic acid residues present within polypeptides (D. W.Cleveland, J. Biol. Chem. 3:1102-1106, 1977). Endoproteinase Asp-N cancleave specifically on the amino side of the asparagine residues presentwithin polypeptides. Endoproteinase Lys-C can cleave specifically on thecarboxyl side of the lysine residues present within polypeptides of theinvention. Other enzymatic and chemical treatments can likewise be usedto specifically fragment these polypeptides into a unique set ofspecific peptides.

Of course, the peptides and fragments of the polypeptides of theinvention can also be produced by conventional recombinant processes andsynthetic processes well known in the art. With regard to recombinantprocesses, the polypeptides and peptide fragments encompassed byinvention can have variable molecular weights, depending upon the hostcell in which they are expressed. Glycosylation of polypeptides andpeptide fragments of the invention in various cell types can result invariations of the molecular weight of these pieces, depending upon theextent of modification. The size of these pieces can be mostheterogeneous with fragments of polypeptide derived from theextracellular portion of the polypeptide. Consistent polypeptides andpeptide fragments can be obtained by using polypeptides derived entirelyfrom the transmembrane and cytoplasmic regions, pretreating withN-glycanase to remove glycosylation, or expressing the polypeptides inbacterial hosts.

The molecular weight of these polypeptides can also be varied by fusingadditional peptide sequences to both the amino and carboxyl terminalends of polypeptides of the invention. Fusions of additional peptidesequences at the amino and carboxyl terminal ends of polypeptides of theinvention can be used to enhance expression of these polypeptides or aidin the purification of the protein. In addition, fusions of additionalpeptide sequences at the amino and carboxyl terminal ends ofpolypeptides of the invention will alter some, but usually not all, ofthe fragmented peptides of the polypeptides generated by enzymatic orchemical treatment. Of course, mutations can be introduced intopolypeptides of the invention using routine and known techniques ofmolecular biology. For example, a mutation can be designed so as toeliminate a site of proteolytic cleavage by a specific enzyme or a siteof cleavage by a specific chemically induced fragmentation procedure.The elimination of the site will alter the peptide fingerprint ofpolypeptides of the invention upon fragmentation with the specificenzyme or chemical procedure.

The polypeptides and the resultant fragmented peptides can be analyzedby methods including sedimentation, electrophoresis, chromatography, andmass spectrometry to determine their molecular weights. Because theunique amino acid sequence of each piece specifies a molecular weight,these pieces can thereafter serve as molecular weight markers using suchanalysis techniques to assist in the determination of the molecularweight of an unknown protein, polypeptides or fragments thereof. Themolecular weight markers of the invention serve particularly well asmolecular weight markers for the estimation of the apparent molecularweight of proteins that have similar apparent molecular weights and,consequently, allow increased accuracy in the determination of apparentmolecular weight of proteins.

When the invention relates to the use of fragmented peptide molecularweight markers, those markers are preferably at least 10 amino acids insize. More preferably, these fragmented peptide molecular weight markersare between 10 and 100 amino acids in size. Even more preferable arefragmented peptide molecular weight markers between 10 and 50 aminoacids in size and especially between 10 and 35 amino acids in size. Mostpreferable are fragmented peptide molecular weight markers between 10and 20 amino acids in size.

Among the methods for determining molecular weight are sedimentation,gel electrophoresis, chromatography, and mass spectrometry. Aparticularly preferred embodiment is denaturing polyacrylamide gelelectrophoresis (U. K. Laemmli, Nature 227:680-685, 1970).Conventionally, the method uses two separate lanes of a gel containingsodium dodecyl sulfate and a concentration of acrylamide between 6-20%.The ability to simultaneously resolve the marker and the sample underidentical conditions allows for increased accuracy. It is understood, ofcourse, that many different techniques can be used for the determinationof the molecular weight of an unknown protein using polypeptides of theinvention, and that this embodiment in no way limits the scope of theinvention.

Each unglycosylated polypeptide or fragment thereof has a pI that isintrinsically determined by its unique amino acid sequence (which pI canbe estimated by the skilled artisan using any of the computer programsdesigned to predict pI values currently available, calculated using anywell-known amino acid pKa table, or measured empirically). Thereforethese polypeptides and fragments thereof can serve as specific markersto assist in the determination of the isoelectric point of an unknownprotein, polypeptide, or fragmented peptide using techniques such asisoelectric focusing. These polypeptide or fragmented peptide markersserve particularly well for the estimation of apparent isoelectricpoints of unknown proteins that have apparent isoelectric points closeto that of the polypeptide or fragmented peptide markers of theinvention.

The technique of isoelectric focusing can be further combined with othertechniques such as gel electrophoresis to simultaneously separate aprotein on the basis of molecular weight and charge. The ability tosimultaneously resolve these polypeptide or fragmented peptide markersand the unknown protein under identical conditions allows for increasedaccuracy in the determination of the apparent isoelectric point of theunknown protein. This is of particular interest in techniques, such astwo dimensional electrophoresis (T. D. Brock and M. T. Madigan, Biologyof Microorganisms 76-77 (Prentice Hall, 6d ed. 1991)), where the natureof the procedure dictates that any markers should be resolvedsimultaneously with the unknown protein. In addition, with such methods,these polypeptides and fragmented peptides thereof can assist in thedetermination of both the isoelectric point and molecular weight of anunknown protein or fragmented peptide.

Polypeptides and fragmented peptides can be visualized using twodifferent methods that allow a discrimination between the unknownprotein and the molecular weight markers. In one embodiment, thepolypeptide and fragmented peptide molecular weight markers of theinvention can be visualized using antibodies generated against thesemarkers and conventional immunoblotting techniques. This detection isperformed under conventional conditions that do not result in thedetection of the unknown protein. It is understood that it may not bepossible to generate antibodies against all polypeptide fragments of theinvention, since small peptides may not contain immunogenic epitopes. Itis further understood that not all antibodies will work in this assay;however, those antibodies which are able to bind polypeptides andfragments of the invention can be readily determined using conventionaltechniques.

The unknown protein is also visualized by using a conventional stainingprocedure. The molar excess of unknown protein to polypeptide orfragmented peptide molecular weight markers of the invention is suchthat the conventional staining procedure predominantly detects theunknown protein. The level of these polypeptide or fragmented peptidemolecular weight markers is such as to allow little or no detection ofthese markers by the conventional staining method. The preferred molarexcess of unknown protein to polypeptide molecular weight markers of theinvention is between 2 and 100,000 fold. More preferably, the preferredmolar excess of unknown protein to these polypeptide molecular weightmarkers is between 10 and 10,000 fold and especially between 100 and1,000 fold.

It is understood of course that many techniques can be used for thedetermination and detection of molecular weight and isoelectric point ofan unknown protein, polypeptides, and fragmented peptides thereof usingthese polypeptide molecular weight markers and peptide fragments thereofand that these embodiments in no way limit the scope of the invention.

In another embodiment, the analysis of the progressive fragmentation ofthe polypeptides of the invention into specific peptides (D. W.Cleveland et al., J. Biol. Chem. 252:1102-1106, 1977), such as byaltering the time or temperature of the fragmentation reaction, can beused as a control for the extent of cleavage of an unknown protein. Forexample, cleavage of the same amount of polypeptide and unknown proteinunder identical conditions can allow for a direct comparison of theextent of fragmentation. Conditions that result in the completefragmentation of the polypeptide can also result in completefragmentation of the unknown protein.

As to the specific use of the polypeptides and fragmented peptides ofthe invention as molecular weight markers, the fragmentation of the IL-1zeta polypeptide of SEQ ID NO:3 with cyanogen bromide generates a uniqueset of fragmented peptide molecular weight markers with molecularweights of approximately 701.7, 2955.4, 5101.8 and 12688.5 Daltons.Additionally, fragmentation of the Xrec2 polypeptide of SEQ ID NO:4 withcyanogen bromide generates the following fragmented peptide molecularweight markers with molecular weights of approximately 2216.7, 2259.6,2376.6, 2738.1, 2901.1, 3417.2, 3627.1, 3656.1, 4042.5, 4144.6, 4668.1,4710.5, 4916.8, 5288.1, 6089.5, 8199.1, and 11919.7 Daltons in theabsence of glycosylation. In the fragmentation of both SEQ ID NOs:3 and4, an additional fragment of 149.2 Daltons results if the initiatingmethionine is present. The distribution of methionine residuesdetermines the number of amino acids in each peptide and the uniqueamino acid composition of each peptide determines its molecular weight.

In addition, the preferred purified polypeptides of the invention (SEQID NOs:3 and 4) have a calculated molecular weight of approximately21542.56 and 79967.85 Daltons, respectively. Thus, where an intactprotein is used, the use of these polypeptide molecular weight markersallows increased accuracy in the determination of apparent molecularweight of proteins that have apparent molecular weights close to21542.56 and 79967.85 Daltons. Where fragments are used, there isincreased accuracy in determining molecular weight over the range of themolecular weights of the fragment.

Finally, as to the kits that are encompassed by the invention, theconstituents of such kits can be varied, but typically contain thepolypeptide and fragmented peptide molecular weight markers. Also, suchkits can contain the polypeptides wherein a site necessary forfragmentation has been removed. Furthermore, the kits can containreagents for the specific cleavage of the polypeptide and the unknownprotein by chemical or enzymatic cleavage. Kits can further containantibodies directed against polypeptides or fragments thereof of theinvention.

Identification of Unknown Proteins

As set forth above, a polypeptide or peptide fingerprint can be enteredinto or compared to a database of known proteins to assist in theidentification of the unknown protein using mass spectrometry (W. J.Henzel et al., Proc. Natl. Acad. Sci. USA 90:5011-5015, 1993; D. Fenyoet al., Electrophoresis 19:998-1005, 1998). A variety of computersoftware programs to facilitate these comparisons are accessible via theInternet, such as Protein Prospector (Internet site:prospector.uscf.edu), MultiIdent (Internet site:www.expasy.ch/sprot/multiident.html), PeptideSearch (Internetsite:www.mann.embl-heiedelberg.de . . . deSearch/FR_PeptideSearchForm.html), and ProFound (Internetsite:www.chait-sgi.rockefeller.edu/cgi-bin/prot-id-frag.html). Theseprograms allow the user to specify the cleavage agent and the molecularweights of the fragmented peptides within a designated tolerance. Theprograms compare observed molecular weights to predicted peptidemolecular weights derived from sequence databases to assist indetermining the identity of the unknown protein.

In addition, a polypeptide or peptide digest can be sequenced usingtandem mass spectrometry (MS/MS) and the resulting sequence searchedagainst databases (J. K. Eng, et al., J. Am. Soc. Mass Spec. 5:976-989(1994); M. Mann and M. Wilm, Anal. Chem. 66:4390-4399 (1994); J. A.Taylor and R. S. Johnson, Rapid Comm. Mass Spec.11:1067-1075 (1997)).Searching programs that can be used in this process exist on theInternet, such as Lutefisk 97 (Internet site:www.lsbc.com:70/Lutefisk97.html), and the Protein Prospector, PeptideSearch and ProFound programs described above.

Therefore, adding the sequence of a gene and its predicted proteinsequence and peptide fragments to a sequence database can aid in theidentification of unknown proteins using mass spectrometry.

Antibodies

Antibodies that are immunoreactive with the polypeptides of theinvention are provided herein. Such antibodies specifically bind to thepolypeptides via the antigen-binding sites of the antibody (as opposedto non-specific binding). Thus, the polypeptides, fragments, variants,fusion proteins, etc., as set forth above may be employed as“immunogens” in producing antibodies immunoreactive therewith. Morespecifically, the polypeptides, fragment, variants, fusion proteins,etc. contain antigenic determinants or epitopes that elicit theformation of antibodies.

These antigenic determinants or epitopes can be either linear orconformational (discontinuous). Linear epitopes are composed of a singlesection of amino acids of the polypeptide, while conformational ordiscontinuous epitopes are composed of amino acids sections fromdifferent regions of the polypeptide chain that are brought into closeproximity upon protein folding (C. A. Janeway, Jr. and P. Travers,Immuno Biology 3:9 (Garland Publishing Inc., 2nd ed. 1996)). Becausefolded proteins have complex surfaces, the number of epitopes availableis quite numerous; however, due to the conformation of the protein andsteric hindrances, the number of antibodies that actually bind to theepitopes is less than the number of available epitopes (C. A. Janeway,Jr. and P. Travers, Immuno Biology 2:14 (Garland Publishing Inc., 2nded. 1996)). Epitopes may be identified by any of the methods known inthe art.

Thus, one aspect of the present invention relates to the antigenicepitopes of the polypeptides of the invention. Such epitopes are usefulfor raising antibodies, in particular monoclonal antibodies, asdescribed in more detail below. Additionally, epitopes from thepolypeptides of the invention can be used as research reagents, inassays, and to purify specific binding antibodies from substances suchas polyclonal sera or supernatants from cultured hybridomas. Suchepitopes or variants thereof can be produced using techniques well knownin the art such as solid-phase synthesis, chemical or enzymatic cleavageof a polypeptide, or using recombinant DNA technology.

As to the antibodies that can be elicited by the epitopes of thepolypeptides of the invention, whether the epitopes have been isolatedor remain part of the polypeptides, both polyclonal and monoclonalantibodies may be prepared by conventional techniques. See, for example,Monoclonal Antibodies, Hybridomas: A New Dimension in BiologicalAnalyses, Kennet et al. (eds.), Plenum Press, New York (1980); andAntibodies: A Laboratory Manual, Harlow and Land (eds.), Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y., (1988).

Hybridoma cell lines that produce monoclonal antibodies specific for thepolypeptides of the invention are also contemplated herein. Suchhybridomas may be produced and identified by conventional techniques.One method for producing such a hybridoma cell line comprises immunizingan animal with a polypeptide; harvesting spleen cells from the immunizedanimal; fusing said spleen cells to a myeloma cell line, therebygenerating hybridoma cells; and identifying a hybridoma cell line thatproduces a monoclonal antibody that binds the polypeptide. Themonoclonal antibodies may be recovered by conventional techniques.

The monoclonal antibodies of the present invention include chimericantibodies, e.g., humanized versions of murine monoclonal antibodies.Such humanized antibodies may be prepared by known techniques and offerthe advantage of reduced immunogenicity when the antibodies areadministered to humans. In one embodiment, a humanized monoclonalantibody comprises the variable region of a murine antibody (or just theantigen binding site thereof) and a constant region derived from a humanantibody. Alternatively, a humanized antibody fragment may comprise theantigen binding site of a murine monoclonal antibody and a variableregion fragment (lacking the antigen-binding site) derived from a humanantibody. Procedures for the production of chimeric and furtherengineered monoclonal antibodies include those described in Riechmann etal. (Nature 332:323, 1988), Liu et al. (PNAS 84:3439, 1987), Larrick etal. (Bio/Technology 7:934, 1989), and Winter and Harris (TIPS 14:139,May, 1993). Procedures to generate antibodies transgenically can befound in GB 2,272,440, U.S. Pat. Nos. 5,569,825 and 5,545,806 andrelated patents claiming priority therefrom, all of which areincorporated by reference herein.

Antigen-binding fragments of the antibodies, which may be produced byconventional techniques, are also encompassed by the present invention.Examples of such fragments include, but are not limited to, Fab andF(ab′)₂ fragments. Antibody fragments and derivatives produced bygenetic engineering techniques are also provided.

In one embodiment, the antibodies are specific for the polypeptides ofthe present invention and do not cross-react with other proteins.Screening procedures by which such antibodies may be identified are wellknown, and may involve immunoaffinity chromatography, for example.

Uses Thereof

The antibodies of the invention can be used in assays to detect thepresence of the polypeptides or fragments of the invention, either invitro or in vivo. The antibodies also may be employed in purifyingpolypeptides or fragments of the invention by immunoaffinitychromatography. Those antibodies that additionally can block binding ofthe polypeptides of the invention to the binding partner may be used toinhibit a biological activity that results from such binding. Suchblocking antibodies may be identified using any suitable assayprocedure, such as by testing antibodies for the ability to inhibitbinding of IL-1 zeta to certain cells expressing the IL-1 zetareceptors. Alternatively, blocking antibodies may be identified inassays for the ability to inhibit a biological effect that results frompolypeptides of the invention binding to their binding partners totarget cells. Antibodies may be assayed for the ability to inhibit IL-1zeta-mediated, Xrec2-mediated, or binding partner-mediated cell lysis,for example. Antibodies that are antagonistic or block IL-1 zetaactivity are useful as therapeutic agents for down-regulating IL-12expression and TNF expression. Thus, such antagonists are useful intreating deleterious affects of inflammation and disease associated withadverse immune responses as described herein. Similarly, agonisticantibodies to IL-1 zeta polypeptide are useful in upregulating IL-12expression and are useful in enhancing the effects of Th1 mediatedimmune response as described herein.

Such an antibody may be employed in an in vitro procedure, oradministered in vivo to inhibit a biological activity mediated by theentity that generated the antibody. Disorders caused or exacerbated(directly or indirectly) by the interaction of the polypeptides of theinvention with the binding partner thus may be treated. A therapeuticmethod involves in vivo administration of a blocking antibody to amammal in an amount effective in inhibiting a binding partner-mediatedbiological activity or a biological activity such as the inhibition ofIL-12 and TNF expression. Monoclonal antibodies are generally preferredfor use in such therapeutic methods. In one embodiment, anantigen-binding antibody fragment is employed.

Antibodies may be screened for agonistic (i.e., ligand-mimicking)properties. Such antibodies, upon binding to cell surface receptor,induce biological effects (e.g., transduction of biological signals)similar to the biological effects induced when IL-1 binds to cellsurface IL-1 receptors. Agonistic antibodies may be used to activateIL-12 expression and treat disease associated with Th1 mediatedpathways.

Compositions comprising an antibody that is directed againstpolypeptides of the invention, and a physiologically acceptable diluent,excipient, or carrier, are provided herein. Suitable components of suchcompositions are as described above for compositions containingpolypeptides of the invention.

Also provided herein are conjugates comprising a detectable (e.g.,diagnostic) or therapeutic agent, attached to the antibody. Examples ofsuch agents are presented above. The conjugates find use in in vitro orin vivo procedures.

Because the IL-1 zeta polypeptides, and particularly the TDZ1 isoform,are active in IL-12 regulation and TNF regulation, inhibitors such assmall molecule inhibitors of its function or its protein associations(or antisense or other inhibitors of its synthesis) will be useful intreating autoimmune and/or inflammatory disorders. Accordingly, IL-1zeta polypeptides and fragments of IL-1 zeta polypeptides that arecapable of upregulating IL-12 production or TNF production as describedbelow, for example, are useful in screening assays to identify compoundsand small molecules which inhibit (antagonize) functions and activitiesof IL-1 zeta polypeptide and described herein. Similarly, IL-1 zetapolypeptides and fragments of IL-1 zeta polypeptides that are capable ofupregulating IL-12 production are useful in screening assays to identifycompounds and small molecules which agonize or enhance IL-12 expression.Such compounds are useful as therapeutics for the herein described usesassociated with enhanced IL-12 expression. (U.S. Pat. No. 5,674,483 andU.S. Pat. No. 5,928,636 which are incorporated herein by reference).

Thus, for example, polypeptides and polypeptide fragments of theinvention may be used to identify antagonists and agonists from cells,cell-free preparations, chemical libraries, and natural productmixtures. The antagonists and agonists may be natural or modifiedsubstrates, ligands, enzymes, receptors, etc. of the polypeptides of theinstant invention, or may be structural or functional mimetics of thepolypeptides. Potential antagonists of the instant invention may includesmall molecules, peptides and antibodies that bind to and occupy abinding site of the inventive polypeptides or a binding partner thereof,causing them to be unavailable to bind to their natural binding partnersand therefore preventing normal biological activity. Potential agonistsinclude small molecules, peptides and antibodies which bind to theinstant polypeptides or binding partners thereof, and elicit the same orenhanced biologic effects as those caused by the binding of thepolypeptides of the instant invention.

Small molecule agonists and antagonists are usually less than 10Kmolecular weight and may possess a number of physicochemical andpharmacological properties which enhance cell penetration, resistdegradation and prolong their physiological half-lives (Gibbs, J.,Pharmaceutical Research in Molecular Oncology, Cell, Vol. 79 (1994)).Antibodies, which include intact molecules as well as fragments such asFab and F(ab′)₂ fragments, as well as recombinant molecules derivedtherefrom, may be used to bind to and inhibit the polypeptides of theinstant invention by blocking the propagation of a signaling cascade. Itis preferable that the antibodies are humanized, and more preferablethat the antibodies are human. The antibodies of the present inventionmay be prepared by any of a variety of well-known methods.

Screening methods are known in the art and along with integrated roboticsystems and collections of chemical compounds/natural products areextensively incorporated in high throughput screening so that largenumbers of test compounds can be tested for antagonist or agonistactivity within a short amount of time. These methods includehomogeneous assay formats such as fluorescence resonance energytransfer, fluorescence polarization, time-resolved fluorescenceresonance energy transfer, scintillation proximity assays, reporter geneassays, fluorescence quenched enzyme substrate, chromogenic enzymesubstrate and electrochemiluminescence, as well as more traditionalheterogeneous assay formats such as enzyme-linked immunosorbant assays(ELISA) or radioimmunoassays.

Homogeneous assays are mix-and-read style assays that are very amenableto robotic application, whereas heterogeneous assays require separationof free from bound analyte by more complex unit operations such asfiltration, centrifugation or washing. These assays are utilized todetect a wide variety of specific biomolecular interactions and theinhibition thereof by small organic molecules, includingprotein-protein, receptor-ligand, enzyme-substrate, and so on. Theseassay methods and techniques are well known in the art (see, e.g., HighThroughput Screening: The Discovery of Bioactive Substances, John P.Devlin (ed.), Marcel Dekker, New York, 1997 ISBN: 0-8247-0067-8). Thescreening assays of the present invention are amenable to highthroughput screening of chemical libraries and are suitable forscreening test compounds in order to identify small molecule drugcandidates, antibodies, peptides, and other antagonists and/or agonists,natural or synthetic.

Thus, a method of the present invention includes screening a testcompound to determine its effect on the ability of a polypeptide of thisinvention to increase or decrease IL-12 expression and/or TNFexpression. Such a method involves co-culturing an IL-1 zeta polypeptideof this invention, particularly the TDZ1 isoform, and cells capable ofexpressing IL-12 and/or TNF (e.g. monocytes, PBMC) and analyzing theculture for IL-12 and/or TNF levels. If the level of expression differsfrom that level of expression that is observed in the absence of testcompound, a test compound that affects IL-12 and/or TNF expression isidentified. Polypeptides that are useful in the screening methodsinclude the IL-1 zeta polypeptides of this invention and fragments ofthe IL-1 zeta polypeptides that upregulate IL-12 expression and/or TNFexpression, particularly the TDZ1 isoform.

In one embodiment of a method for identifying molecules which inhibit orantagonize the polypeptides of this invention involves adding a testcompound to a medium which contains cells that express the polypeptidesof the instant invention; changing the conditions of the medium so that,but for the presence of the test compound, the polypeptides would bebound to their natural ligands, substrates or effector molecules, andobserving the binding and stimulation or inhibition of a functionalresponse. The activity of the cells which were contacted with the testcompound may then be compared with the identical cells which were notcontacted and antagonists and agonists of the polypeptides of theinstant invention may be identified. The measurement of biologicalactivity may be performed by a number of well-known methods such asmeasuring the amount of protein present (e.g. an ELISA) or measuring theprotein's activity. A decrease in biological stimulation or activationindicates an antagonist. An increase indicates an agonist.

Another embodiment of the invention relates to uses of polypeptides ofthis invention to study cell signal transduction. Cellular signalingoften involves a molecular activation cascade, during which a receptorpropagates a ligand-receptor mediated signal by specifically activatingintracellular kinases which phosphorylate target substrates. Thesesubstrates can themselves be kinases which become activated followingphosphorylation. Alternatively, they can be adapter molecules thatfacilitate down stream signaling through protein-protein interactionfollowing phosphorylation. Accordingly, these polypeptides and activefragments can be used as reagents to identify novel molecules involvedin signal transduction pathways.

As therapeutics, inhibitors or agonists of IL-1 zeta activity can beadministered to agonize or antagonize IL-1 zeta activity, thus providinguseful immunoregulators. Various liposome-based compositions of theinventive polypeptides are envisioned herein.

Inhibitors and enhancers of the polypeptides or polypeptide fragmentshaving biological activity are useful in treating a variety of medicalconditions. IL-1 zeta polypeptides are associated with IL-12 productionand dysregulation of IL-12 production, and thus agonists of IL-1 zetapolypeptides are useful for treating diseases and medical conditionsthat are therapeutically responsive to IL-12 expression. Such diseasesand medical conditions include infectious diseases, such as HIV,Hepatitis B and Hepatitis C, papilloma, etc.; and, bacterial infections,including tuberculosis, salmonellosis, listeriousis; and, parasiticinfections such as malaria, leishmaniasis and schistosomiasis. Agonistsare also useful for treating dysregulated immune response, e.g. use as avaccine (e.g. for use in connection with antigen such as for measlesvaccination) or vaccine adjuvant, increased response to bacterial andviral infection, as just discussed, and as therapeutic immunotherapiesincluding anticancer immunotherapy treatments. (See U.S. Pat. Nos.6,086,876, and 6,168,923 both of which are incorporated herein byreference) In another embodiment, agonists of IL-1 zeta polypeptides canbe administered in combination with other agents or cytokines fortreating disease and medical conditions. For example, agonists can beadministered in combination with IFN or IFN alpha. Antagonists of IL-1zeta polypeptides are useful in treating certain types of immune systemdysfunction associated with IL-12 dysregulation such as autoimmunediseases, inflammatory conditions, complications that are associatedwith bacterial infections that occur with increased IL-12 activity andconditions associated with increased expression or activity of IL-12.Thus, therapeutics discovered by screening IL-1 zeta polypeptides, theTDZ1 isoform and active fragments for agonistic or antagonistic activityhave properties that make them suitable for use as: anti-inflammatory,anti-tumor or anti-cancer, anti-bacterial, and anti-viral.

Compositions of the present invention may contain a polypeptide or andantagonist or agonist in any form described herein, such as nativeproteins, variants, derivatives, oligomers, biologically activefragments of the compounds described herein, small molecules,antibodies, etc. In particular embodiments, the composition comprisespeptides, small molecules, antibodies or oligomers comprising solublepolypeptides.

Compositions comprising an effective amount of a polypeptide of thepresent invention, in combination with other components such as aphysiologically acceptable diluent, carrier, or excipient, are providedherein. The polypeptides can be formulated according to known methodsused to prepare pharmaceutically useful compositions. They can becombined in admixture, either as the sole active material or with otherknown active materials suitable for a given indication, withpharmaceutically acceptable diluents (e.g., saline, Tris-HCl, acetate,and phosphate buffered solutions), preservatives (e.g., thimerosal,benzyl alcohol, parabens), emulsifiers, solubilizers, adjuvants and/orcarriers. Suitable formulations for pharmaceutical compositions includethose described in Remington's Pharmaceutical Sciences, 16th ed. 1980,Mack Publishing Company, Easton, Pa.

In addition, such compositions can be complexed with polyethylene glycol(PEG), metal ions, or incorporated into polymeric compounds such aspolyacetic acid, polyglycolic acid, hydrogels, dextran, etc., orincorporated into liposomes, microemulsions, micelles, unilamellar ormultilamellar vesicles, erythrocyte ghosts or spheroblasts. Suchcompositions will influence the physical state, solubility, stability,rate of in vivo release, and rate of in vivo clearance, and are thuschosen according to the intended application.

The compositions of the invention can be administered in any suitablemanner, e.g., topically, parenterally, orally, intracranially or byinhalation. The term “parenteral” includes injection, e.g., bysubcutaneous, intravenous, or intramuscular routes, also includinglocalized administration, e.g., at a site of disease or injury (forexample, intracoronary or intra tumor administration or injection into ajoint undergoing an inflammatory reaction). Sustained release fromimplants is also contemplated. One skilled in the pertinent art willrecognize that suitable dosages will vary, depending upon such factorsas the nature of the disorder to be treated, the patient's body weight,age, and general condition, and the route of administration. Preliminarydoses can be determined according to animal tests, and the scaling ofdosages for human administration is performed according to art-acceptedpractices.

Moreover, it has been found that DNA encoding a polypeptide can beadministered to a mammal in such a way that it is taken up by cells, andexpressed. The resultant protein will then be available to exert atherapeutic effect. Accordingly, compositions comprising nucleic acidsin physiologically acceptable formulations are also contemplated. DNAmay be formulated for injection, for example.

The following examples are provided to further illustrate particularembodiments of the invention, and are not to be construed as limitingthe scope of the present invention.

EXAMPLE 1 Isolation of the IL-1 zeta and Xrec2 Nucleic Acids

Human IL-1 zeta nucleic acid sequence was obtained by sequencing ESTIMAGE clone 1628761, accession #AI014548, which encoded a partial openreading frame (ORF). A number of cDNA libraries were screened withinternal primers to determine the expression pattern of the polypeptide.After performing PCR using two internal primers of human IL-1 zetasequence, the following cDNA libraries were positive for IL-1 zetasequences: bone marrow stromal, human pancreatic tumor, and Raji. IL-1zeta clones were isolated from human genomic DNA sequences, bone marrowstromal and human pancreatic tumor libraries, and sequenced.

Human Xrec2 sequences were obtained by high-throughput sequencing, PCR,and 5′ RACE reactions. High-throughput shotgun sequencing of chromosomeregion Xp11 yielded sequences for exons 4-6 of Xrec2 (Genbank accessionnumbers AL031466 and AL031575). Similarly, sequence of chromosome regionXp22-164-166 (Genbank accession number AC005748) yielded sequences forexons 10-12 of Xrec2.

PCR performed on human brain first strand cDNA using primers withinexons 5 and 11 generated sequence for exons 7-9. 5′ RACE reactions werethen performed using testis cDNA and nested primers within exon 4 toobtain exon 3 sequences which contained the predicted initiatormethionine. Both PCR and the 5′ RACE reactions were performed usingstandard protocols.

EXAMPLE 2 Use of Purified IL-1 zeta and Xrec2 PolypeptidesPolypeptide-Specific ELISA

Serial dilutions of IL-1 zeta- or Xrec2-containing samples (in 50 mMNaHCO₃, brought to pH 9 with NaOH) are coated onto Linbro/Titertek 96well flat bottom E.I.A. microtitration plates (ICN Biomedicals Inc.,Aurora, Ohio) at 100:1/well. After incubation at 4EC for 16 hours, thewells are washed six times with 200:1 PBS containing 0.05% Tween-20(PBS-Tween). The wells are then incubated with FLAG7-binding partner at1 mg/ml in PBS-Tween with 5% fetal calf serum (FCS) for 90 minutes(100:1 per well), followed by washing as above. Next, each well isincubated with the anti-FLAG7 (monoclonal antibody M2 at 1 mg/ml inPBS-Tween containing 5% FCS for 90 minutes (100:1 per well), followed bywashing as above. Subsequently, wells are incubated with a polyclonalgoat anti-mIgG1-specific horseradish peroxidase-conjugated antibody (a1:5000 dilution of the commercial stock in PBS-Tween containing 5% FCS)for 90 minutes (100:1 per well). The HRP-conjugated antibody is obtainedfrom Southern Biotechnology Associates, Inc., Birmingham, Ala. Wellsthen are washed six times, as above.

For development of the ELISA, a substrate mix [100:1 per well of a 1:1premix of the TMB Peroxidase Substrate and Peroxidase Solution B(Kirkegaard Perry Laboratories, Gaithersburg, Md.)] is added to thewells. After sufficient color reaction, the enzymatic reaction isterminated by addition of 2 N H₂SO₄ (50:1 per well). Color intensity(indicating ligand receptor binding) is determined by measuringextinction at 450 nm on a V Max plate reader (Molecular Devices,Sunnyvale, Calif.).

EXAMPLE 3 Amino Acid Sequence

The amino acid sequence of IL-1 zeta and Xrec2 were determined bytranslation of the complete nucleotide sequences of SEQ ID NOs:1 and 2,respectively.

EXAMPLE 4 DNA and Amino Acid Sequences

The IL-1 zeta and Xrec2 nucleic acid sequences were determined bystandard double stranded sequencing of the composite sequence of ESTIMAGE clones (accession #AI014548 (IL-1 zeta) and # AL031575 and#AC005748 (Xrec2)), and of additional sequences obtained from PCR and 5′RACE reactions.

The nucleotide sequence of the isolated IL-1 zeta and Xrec2 DNA and theamino acid sequence encoded thereby, are presented in SEQ ID NOs:1-4.The sequence of the IL-1 zeta DNA fragment isolated by PCR correspondsto nucleotides 1 to 579 of SEQ ID NO: 1, which encode amino acids 1 to192 of SEQ ID NO:3; and the sequence of the Xrec2 DNA fragment alsoisolated by PCR corresponds to nucleotides 1 to 2088 of SEQ ID NO:2,which encode amino acids 1 to 698 of SEQ ID NO:4.

The amino acid sequences of SEQ ID NOs:3 and 4 bear significant homologyto other known IL-1 ligand and receptor family members, respectively.

EXAMPLE 5 Monoclonal Antibodies that Bind Polypeptides of the Invention

This example illustrates a method for preparing monoclonal antibodiesthat bind IL-1 zeta. The same protocol can be used to produce monoclonalantibodies that bind Xrec2. Suitable immunogens that may be employed ingenerating such antibodies include, but are not limited to, purifiedIL-1 zeta polypeptide or an immunogenic fragment thereof such as theextracellular domain, or fusion proteins containing 1L-1 zeta (e.g., asoluble IL-1 zeta/Fc fusion protein).

Purified IL-1 zeta can be used to generate monoclonal antibodiesimmunoreactive therewith, using conventional techniques such as thosedescribed in U.S. Pat. No. 4,411,993. Briefly, mice are immunized withIL-1 zeta immunogen emulsified in complete Freund's adjuvant, andinjected in amounts ranging from 10-100 g subcutaneously orintraperitoneally. Ten to twelve days later, the immunized animals areboosted with additional IL-1 zeta emulsified in incomplete Freund'sadjuvant. Mice are periodically boosted thereafter on a weekly tobi-weekly immunization schedule. Serum samples are periodically taken byretro-orbital bleeding or tail-tip excision to test for IL-1 zetaantibodies by dot blot assay, ELISA (Enzyme-Linked immunosorbent Assay)or inhibition of IL-1 zeta receptor binding.

Following detection of an appropriate antibody titer, positive animalsare provided one last intravenous injection of IL-1 zeta in saline.Three to four days later, the animals are sacrificed, spleen cellsharvested, and spleen cells are fused to a murine myeloma cell line,e.g., NS1 or preferably P3x63Ag8.653 (ATCC CRL 1580). Fusions generatehybridoma cells, which are plated in multiple microtiter plates in a HAT(hypoxanthine, aminopterin and thymidine) selective medium to inhibitproliferation of non-fused cells, myeloma hybrids, and spleen cellhybrids.

The hybridoma cells are screened by ELISA for reactivity againstpurified IL-1 zeta by adaptations of the techniques disclosed in Engvallet al., (Immunochem. 8:871, 1971) and in U.S. Pat. No. 4,703,004. Apreferred screening technique is the antibody capture techniquedescribed in Beckmann et al., (J. Immunol. 144:4212, 1990). Positivehybridoma cells can be injected intraperitoneally into syngeneic BALB/cmice to produce ascites containing high concentrations of anti-IL-1 zetamonoclonal antibodies. Alternatively, hybridoma cells can be grown invitro in flasks or roller bottles by various techniques. Monoclonalantibodies produced in mouse ascites can be purified by ammonium sulfateprecipitation, followed by gel exclusion chromatography. Alternatively,affinity chromatography based upon binding of antibody to Protein A orProtein G can also be used, as can affinity chromatography based uponbinding to IL-1 zeta.

EXAMPLE 6 Northern Blot Analysis

The tissue distribution of IL-1 zeta and Xrec2 mRNA is investigated byNorthern blot analysis, as follows. An aliquot of a radiolabeled probeis added to two different human multiple tissue Northern blots(Clontech, Palo Alto, Calif.; Biochain, Palo Alto, Calif.). The blotsare hybridized in 10× Denhardts, 50 mM Tris pH 7.5, 900 mM NaCl, 0.1% Napyrophosphate, 1% SDS, 2001 g/mL salmon sperm DNA. Hybridization isconducted overnight at 63EC in 50% formamide as previously described(March et al., Nature 315:641-647, 1985). The blots are then washed with2×SSC, 0.1% SDS at 68EC for 30 minutes. The cells and tissues with thehighest levels of IL-1 zeta and Xrec2 mRNA are determined by comparisonto control probing with a α-actin-specific probe.

EXAMPLE 7 Binding Assay

Full length IL-1 zeta can be expressed and tested for the ability tobind IL-1 zeta receptors. The binding assay can be conducted as follows.

A fusion protein comprising a leucine zipper peptide fused to theN-terminus of a soluble IL-1 zeta polypeptide (LZ-IL-1 zeta) is employedin the assay. An expression construct is prepared, essentially asdescribed for preparation of the FLAG⁷(IL-1 zeta) expression constructin Wiley et al. (Immunity, 3:673-682, 1995; hereby incorporated byreference), except that DNA encoding the FLAG⁷ peptide was replaced witha sequence encoding a modified leucine zipper that allows fortrimerization. The construct, in expression vector pDC409, encodes aleader sequence derived from human cytomegalovirus, followed by theleucine zipper moiety fused to the N-terminus of a soluble IL-1 zetapolypeptide. The LZ-IL-1 zeta is expressed in CHO cells, and purifiedfrom the culture supernatant.

The expression vector designated pDC409 is a mammalian expression vectorderived from the pDC406 vector described in McMahan et al. (EMBO J.10:2821-2832, 1991; hereby incorporated by reference). Features added topDC409 (compared to pDC406) include additional unique restriction sitesin the multiple cloning site (mcs); three stop codons (one in eachreading frame) positioned downstream of the mcs; and a T7 polymerasepromoter, downstream of the mcs, that facilitates sequencing of DNAinserted into the mcs.

For expression of full length human IL-1 zeta protein, the entire codingregion (i.e., the DNA sequence presented in SEQ ID NO: 1) is amplifiedby polymerase chain reaction (PCR). The template employed in the PCR isthe cDNA clone isolated from a (pancreatic tumor) cDNA library, asdescribed in example 1. The isolated and amplified DNA is inserted intothe expression vector pDC409, to yield a construct designatedpDC409-IL-1 zeta.

LZ-IL-1 zeta polypeptide is employed to test the ability to bind to hostcells expressing recombinant or endogenous IL-1 zeta receptors, asdiscussed above. Cells expressing IL-1 zeta receptor are cultured inDMEM supplemented with 10% fetal bovine serum, penicillin, streptomycin,and glutamine. Cells are incubated with LZ-IL-1 zeta (5 mg/ml) for about1 hour. Following incubation, the cells are washed to remove unboundLZ-IL-1 zeta and incubated with a biotinylated anti-LZ monoclonalantibody (5 mg/ml), and phycoerythrin-conjugated streptavidin (1:400),before analysis by fluorescence-activated cell scanning (FACS). Thecytometric analysis was conducted on a FACscan (Beckton Dickinson, SanJose, Calif.).

The cells expressing IL-1 zeta receptors showed significantly enhancedbinding of LZ-IL-1 zeta, compared to the control cells not expressingIL-1 zeta receptors.

EXAMPLE 8 Obtaining TDZ.1, TDZ.2, and TDZ.3 and Tissue Distribution

In order to determine and study the relative abundance and tissuedistribution of Tango-77 (WO 99/06426), an alternatively spliced form ofIL-1 zeta, and IL-1 zeta, RT-PCR was performed. The primers used in theRT PCR were 5′ primers specific for either Tango-77 exon #1 (see FIG. 1)or IL-1 zeta exon #1 (exons #3 in FIG. 1) in combination with a common3′ primer from the common final exon (exon #6 in FIG. 1). The PCRreactions were performed using first strand cDNA from multiple humantissue sources purchased from Clontech, Palo Alto, Calif. The PCRreaction generated PCR products that included the predicted size productand additional bands. In particular, three different sized PCR productswere isolated and used to obtain sequence information from multipletissue cDNAs. The sequences of these three products, SEQ ID NOs:5, 6, 7and encoded amino acids of SEQ ID NO:8, 9, and 10, are splice variants.The organization the relationship of these splice variants are shown inFIG. 1 and discussed above. The splice variants are TDZ.1, TDZ.2, andTDZ.3 (Testis-Derived Zeta variants) because all three of them areexpressed in testis. Testis is a common expression tissue. However, itis not the only expression tissue. Table II describes the results of thetissue expression study for Tango-77, IL-1 zeta, TDZ.1, TDZ.2, andTDZ.3. TDZ.1 and TDZ.2 contain exons 4, 5 and 6 which correspond to thelast three exons of IL-1 zeta and correspond to the conserved structuraldomain of the molecule. As discussed above, when aligned with othermembers of the IL-1 family, exons 4, 5 and 6 are shown to contain manyconserved residues within conserved structural motifs.

A polymorphism of Tango 77 in exon #2 of FIG. 1 is noted. In theisolated cDNAS a valine occurs in lieu of a glycine at the third residueof exon #2. In the Tango-77 sequence, the amino acid sequence isPAGSPLEP. In the polymorphism the sequence is PAVSPLEP.

Tissue Distribution of FIL-1Z Splice Variants TABLE II Tissue IL-1zTango-77 TDZ.1 TDZ.2 TDZ.3 kidney − − + − − pancreas − − − − − skeletalmuscle − − + − − heart − + − − − testis + + + + + prostrate + − + − −spleen − − − − − ovary − + + − − thymus − − − − − colon + + + − −leukocytes − − − − − small intestine − + + − − liver − + + − − brain + −− − − placenta + + + − + lung + + + − + tonsil − + + − − fetalliver + + + − − lymph node + + + − − bone marrow − + + + +

EXAMPLE 9 IL-1 Zeta Polypeptide Induces TNF and IL-12 Secretion

The following assays were performed to study cytokine induction by IL-1Zeta polypeptides. A protein of IL-1 zeta, TDZ.1 isoform, fused to aFLAG-poly His polypeptide at its C-terminus, was prepared andco-cultured with human monocytes. Varying concentrations of the TDZ.1isoform were used with a lower level concentration of 5 nM. The culturewas analyzed for cytokines and found to have increased levels ofTNF-alpha and IL-12. This cytokine inducing activity was dose dependent.

The references cited herein are incorporated by reference herein intheir entirety.

1. An isolated polynucleotide comprising a polynucleotide of SEQ IDNO:6.
 2. An isolated polynucleotide comprising a nucleic acid moleculethat encodes a polypeptide comprising SEQ ID NO:9.
 3. A vectorcomprising the polynucleotide of claim
 1. 4. A vector comprising thepolynucleotide of claim
 2. 5. A host cell transformed or transfectedwith the vector of claim
 3. 6. A host cell transformed or transfectedwith the vector of claim
 4. 7. A method for preparing a polypeptide, themethod comprising culturing the host cell of claim 5 under conditionspromoting expression of the polypeptide.
 8. A method for preparing apolypeptide, the method comprising culturing the host cell of claim 6under conditions promoting expression of the polypeptide.
 9. An isolatedpolypeptide comprising SEQ ID NO:9.
 10. An oligomeric polypeptidecomprising a polypeptide of claim
 9. 11. A method for screening a testcompound to determine its effect on the ability of a IL-1 zetapolypeptide to increase or decrease IL-12 expression and or TNF-alphaexpression, the method comprising: a) contacting a test compound and anIL-1 zeta polypeptide according to claim 9 with cells capable ofexpressing IL-12 and/or TNF; and, b) analyzing the culture for IL-12and/or TNF, wherein, if the IL-12 or TNF expression differs from thelevel of expression that is observed in the absence of test compound,the test compound affects IL-12 and/or TNF expression.
 12. A method forincreasing EL-12 production in an individual, the method comprisingadministering an IL-1 zeta polypeptide according to claim 9 to theindividual in an amount sufficient to increase IL-12 production.